diff --git a/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/eclipselink-incubator-fetchplan.jar b/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/eclipselink-incubator-fetchplan.jar
index f2e10bc..a9a45a9 100644
--- a/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/eclipselink-incubator-fetchplan.jar
+++ b/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/eclipselink-incubator-fetchplan.jar
Binary files differ
diff --git a/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/example.jpa.employee.xml/model/Address.java b/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/example.jpa.employee.xml/model/Address.java
index 5cd52db..4b99ac5 100644
--- a/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/example.jpa.employee.xml/model/Address.java
+++ b/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/example.jpa.employee.xml/model/Address.java
@@ -74,4 +74,8 @@
     public void setStreet(String street) {
         this.street = street;
     }
+
+    public String toString() {
+        return "Address(" + getId() + ")";
+    }
 }
diff --git a/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/src/example/FetchPlanExamples.java b/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/src/example/FetchPlanExamples.java
index 4a025ff..c16bb83 100644
--- a/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/src/example/FetchPlanExamples.java
+++ b/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/src/example/FetchPlanExamples.java
@@ -42,14 +42,15 @@
         fetchPlan.addAttribute("salary");
         fetchPlan.addAttribute("address");
         fetchPlan.addAttribute("phoneNumbers");
-
+        
         Query query = em.createQuery("SELECT e FROM Employee e WHERE e.salary > 0");
-
+        
         // Configure a dynamic FetchGroup based on the FetchPlan
         query.setHint(QueryHints.FETCH_GROUP, fetchPlan.createFetchGroup());
-
+        
         List<Employee> emps = query.getResultList();
-
+        
+        // Force the fetch operation on the query result
         JpaFetchPlanHelper.fetch(em, fetchPlan, emps);
 
         return emps;
@@ -191,15 +192,15 @@
      */
     public List<Employee> employeeCopyWithNamesAddressAndPhones(EntityManager em) {
         Query query = em.createQuery("SELECT e FROM Employee e WHERE e.salary > 0");
-
+        
         FetchPlan fetchPlan = new FetchPlan(Employee.class);
         fetchPlan.addAttribute("firstName");
         fetchPlan.addAttribute("lastName");
         fetchPlan.addAttribute("address");
         fetchPlan.addAttribute("phoneNumbers");
-
+        
         List<Employee> emps = query.getResultList();
-
+        
         return JpaFetchPlanHelper.copy(em, fetchPlan, emps);
     }
 
@@ -279,9 +280,7 @@
         fetchPlan.addAttribute("address");
         fetchPlan.addAttribute("phoneNumbers");
 
-        int minId = ((Number) em.createQuery("SELECT MIN(e.id) FROM Employee e").getSingleResult()).intValue();
-
-        Query query = em.createQuery("SELECT e FROM Employee e WHERE e.id = " + minId);
+        Query query = em.createQuery("SELECT e FROM Employee e WHERE e.id = (SELECT MIN(ee.id) FROM Employee ee)");
         query.setHint(QueryHints.FETCH_GROUP, fetchPlan.createFetchGroup());
 
         Employee emp = (Employee) query.getSingleResult();
@@ -291,6 +290,11 @@
         copy.setSalary(Integer.MAX_VALUE);
         copy.setFirstName(emp.getLastName());
         copy.setLastName(emp.getFirstName());
+        
+        if (clear) {
+            em.clear();
+            JpaHelper.getEntityManager(em).getServerSession().getIdentityMapAccessor().initializeAllIdentityMaps();
+        }
 
         JpaFetchPlanHelper.merge(em, fetchPlan, copy);
     }
diff --git a/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/src/org/eclipse/persistence/extension/query/BatchInConfig.java b/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/src/org/eclipse/persistence/extension/query/BatchInConfig.java
index b12de37..f0418b1 100644
--- a/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/src/org/eclipse/persistence/extension/query/BatchInConfig.java
+++ b/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/src/org/eclipse/persistence/extension/query/BatchInConfig.java
@@ -23,6 +23,7 @@
 import org.eclipse.persistence.indirection.IndirectContainer;
 import org.eclipse.persistence.indirection.ValueHolderInterface;
 import org.eclipse.persistence.internal.indirection.BatchValueHolder;
+import org.eclipse.persistence.internal.indirection.QueryBasedValueHolder;
 import org.eclipse.persistence.internal.indirection.UnitOfWorkValueHolder;
 import org.eclipse.persistence.internal.sessions.AbstractSession;
 import org.eclipse.persistence.jpa.JpaHelper;
@@ -33,7 +34,6 @@
 import org.eclipse.persistence.mappings.OneToOneMapping;
 import org.eclipse.persistence.queries.ReadAllQuery;
 import org.eclipse.persistence.queries.ReadQuery;
-import org.eclipse.persistence.sessions.server.Server;
 
 /**
  * This is an extension to EclipseLink intending to assist customers who need to
@@ -84,7 +84,7 @@
             return;
         }
 
-        Server session = JpaHelper.getEntityManager(em).getServerSession();
+        AbstractSession session = JpaHelper.getEntityManager(em).getServerSession();
         ClassDescriptor descriptor = session.getClassDescriptor(results.get(0));
 
         if (descriptor == null) {
@@ -105,7 +105,7 @@
             throw new IllegalArgumentException("Invalid mapping type found: " + mapping);
         }
 
-        BatchValueHolder batchVH = getBatchValueHolder(frMapping, results);
+        BatchValueHolder batchVH = getBatchValueHolder(frMapping, results, (AbstractSession) session);
 
         if (batchVH == null) {
             SessionLog log = JpaHelper.getEntityManager(em).getServerSession().getSessionLog();
@@ -123,7 +123,7 @@
     /**
      * Find the first BatchValueHolder in the results
      */
-    private static BatchValueHolder getBatchValueHolder(ForeignReferenceMapping mapping, List<?> results) {
+    private static BatchValueHolder getBatchValueHolder(ForeignReferenceMapping mapping, List<?> results, AbstractSession session) {
         Object result = results.get(0);
 
         Object value = mapping.getAttributeValueFromObject(result);
@@ -140,14 +140,18 @@
             return (BatchValueHolder) value;
         }
 
-        // No BatchValueHolder found? TODO: Build one?
-        return null;
+        if (value instanceof QueryBasedValueHolder) {
+            replaceQueryBasedValueHolders(mapping, results, session);
+            return getBatchValueHolder(mapping, results, session);
+        }
+
+        throw new IllegalStateException("TODO: How can we get here?");
     }
 
     /**
      * Customize the query for a 1:1 or M:1
      */
-    private static void configBatchInQuery(Server session, OneToOneMapping mapping, ReadAllQuery raq, List<?> results) {
+    private static void configBatchInQuery(AbstractSession session, OneToOneMapping mapping, ReadAllQuery raq, List<?> results) {
         if (mapping.getForeignKeyFields().size() != 1) {
             throw new IllegalArgumentException("Cannot configure batch using IN with composite FK: " + mapping);
         }
@@ -159,7 +163,7 @@
             if (vhi instanceof UnitOfWorkValueHolder) {
                 vhi = ((UnitOfWorkValueHolder) vhi).getWrappedValueHolder();
             }
-            BatchValueHolder bvh = (BatchValueHolder) vhi;
+            QueryBasedValueHolder bvh = (QueryBasedValueHolder) vhi;
 
             ids[index] = bvh.getRow().get(mapping.getForeignKeyFields().get(0));
         }
@@ -173,12 +177,12 @@
     /**
      * Customize the query for a 1:M
      */
-    private static void configBatchInQuery(Server session, OneToManyMapping mapping, ReadAllQuery raq, List<?> results) {
+    private static void configBatchInQuery(AbstractSession session, OneToManyMapping mapping, ReadAllQuery raq, List<?> results) {
         if (raq == null) {
             // TODO: This occurs when there is no query available.
             return;
         }
-        
+
         if (mapping.getTargetForeignKeyFields().size() != 1) {
             throw new IllegalArgumentException("Cannot configure batch using IN with composite FK: " + mapping);
         }
@@ -224,9 +228,32 @@
 
         ReadQuery batchQuery = frMapping.prepareNestedBatchQuery(raq);
         Object value = frMapping.getIndirectionPolicy().valueFromBatchQuery(batchQuery, null, raq);
-        
-        for (Object result: results) {
+
+        for (Object result : results) {
             frMapping.setAttributeValueInObject(result, value);
         }
     }
+
+    /**
+     * Replace All existing {@link QueryBasedValueHolder} in a set of entities
+     * for the provided mapping with {@link BatchValueHolder} that are later
+     * updated to use the IN operation.
+     */
+    private static void replaceQueryBasedValueHolders(ForeignReferenceMapping mapping, List<?> results, AbstractSession session) {
+        // Create fake source query
+        ReadAllQuery sourceQuery = new ReadAllQuery(mapping.getDescriptor().getJavaClass());
+        sourceQuery.setSession(session);
+        sourceQuery.setDescriptor(mapping.getDescriptor());
+
+        ReadQuery batchQuery = mapping.prepareNestedBatchQuery(sourceQuery);
+
+        for (Object obj : results) {
+            ValueHolderInterface vhi = (ValueHolderInterface) mapping.getAttributeValueFromObject(obj);
+            if (vhi instanceof UnitOfWorkValueHolder) {
+                vhi = ((UnitOfWorkValueHolder) vhi).getWrappedValueHolder();
+            }
+            Object batchVH = mapping.getIndirectionPolicy().valueFromBatchQuery(batchQuery, ((QueryBasedValueHolder) vhi).getRow(), sourceQuery);
+            mapping.setAttributeValueInObject(obj, batchVH);
+        }
+    }
 }
diff --git a/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/test-src/test/FetchPlanFetchWithBatchInTests.java b/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/test-src/test/FetchPlanFetchWithBatchInTests.java
index 9d27a69..cee17f7 100644
--- a/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/test-src/test/FetchPlanFetchWithBatchInTests.java
+++ b/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/test-src/test/FetchPlanFetchWithBatchInTests.java
@@ -12,7 +12,7 @@
  ******************************************************************************/
 package test;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.*;
 
 import java.util.ArrayList;
 import java.util.HashSet;
@@ -136,7 +136,7 @@
     public void findEmployeesWithBatchInConfigFetch() {
         EntityManager em = getEntityManager();
 
-        Query q = em.createQuery("SELECT em FROM Employee em");
+        Query q = em.createQuery("SELECT em FROM Employee em ORDER BY em.id");
         q.setHint(QueryHints.BATCH, "em.managedEmployees");
         q.setHint(QueryHints.BATCH, "em.managedEmployees.address");
 
@@ -153,7 +153,7 @@
         fp.addAttribute("managedEmployees");
         JpaFetchPlanHelper.fetch(em, fp, ems);
 
-        // interate through all employees and collect their managers
+        // iterate through all employees and collect their managers
         Set<Employee> managedEmployees = new HashSet<Employee>();
         for (Employee employee : ems) {
             managedEmployees.addAll(employee.getManagedEmployees());
@@ -165,6 +165,120 @@
         fp2.addAttribute("address");
         JpaFetchPlanHelper.fetch(em, fp2, managedEmployees);
 
+        assertEquals(3, getQuerySQLTracker(em).getTotalSQLSELECTCalls());
+
+        System.out.println("Employees Read - " + ems.size());
+        for (Employee emp : ems) {
+            System.out.println("\t> " + emp);
+            for (Employee managedEmp : emp.getManagedEmployees()) {
+                System.out.println("\t\t> " + managedEmp);
+                System.out.println("\t\t\t> " + managedEmp.getAddress());
+            }
+            if (emp.getManagedEmployees() == null) {
+
+            }
+        }
+
+        assertEquals(3, getQuerySQLTracker(em).getTotalSQLSELECTCalls());
+
+        em.clear();
+        JpaHelper.getServerSession(getEMF()).getIdentityMapAccessor().initializeAllIdentityMaps();
+
+        q = em.createNativeQuery("SELECT EMP_ID, ADDR_ID, MANAGER_ID FROM EMPLOYEE ORDER BY EMP_ID");
+        List<Object[]> ids = q.getResultList();
+
+        assertEquals(4, getQuerySQLTracker(em).getTotalSQLSELECTCalls());
+        assertEquals(ems.size(), ids.size());
+
+        for (int index = 0; index < ems.size(); index++) {
+            Employee emp = ems.get(index);
+            Object[] idRow = ids.get(index);
+
+            assertEquals(emp.getId(), ((Number) idRow[0]).intValue());
+            if (idRow[2] != null) { // We have a manager
+                assertNotNull(emp.getAddress());
+                assertEquals(emp.getAddress().getId(), ((Number) idRow[1]).intValue());
+            } else {
+
+            }
+        }
+    }
+
+    /**
+     * This test does not used BatchIn but is here to provide a verification for
+     * the assertions of {@link #findEmployeesWithBatchInConfigFetch()}
+     */
+    @SuppressWarnings("unchecked")
+    @Test
+    public void findEmployeesWithJoinBatching() {
+        EntityManager em = getEntityManager();
+
+        Query q = em.createQuery("SELECT em FROM Employee em ORDER BY em.id");
+        q.setHint(QueryHints.BATCH, "em.managedEmployees");
+        q.setHint(QueryHints.BATCH, "em.managedEmployees.address");
+
+        List<Employee> ems = q.getResultList();
+
+        // Display initial Employees read:
+        System.out.println("Employees Read - " + ems.size());
+        for (Employee emp : ems) {
+            System.out.println("\t> " + emp);
+        }
+
+        //BatchInConfig.config(em, ems, "managedEmployees");
+        FetchPlan fp = new FetchPlan(Employee.class);
+        fp.addAttribute("managedEmployees");
+        JpaFetchPlanHelper.fetch(em, fp, ems);
+
+        // iterate through all employees and collect their managers
+        Set<Employee> managedEmployees = new HashSet<Employee>();
+        for (Employee employee : ems) {
+            managedEmployees.addAll(employee.getManagedEmployees());
+        }
+
+        // Fetch for all managers the addresses
+        //BatchInConfig.config(em, new ArrayList<Employee>(managedEmployees), "address");
+        FetchPlan fp2 = new FetchPlan(Employee.class);
+        fp2.addAttribute("address");
+        JpaFetchPlanHelper.fetch(em, fp2, managedEmployees);
+
+        assertEquals(13, getQuerySQLTracker(em).getTotalSQLSELECTCalls());
+
+        System.out.println("Employees Read - " + ems.size());
+        for (Employee emp : ems) {
+            System.out.println("\t> " + emp);
+            for (Employee managedEmp : emp.getManagedEmployees()) {
+                System.out.println("\t\t> " + managedEmp);
+                System.out.println("\t\t\t> " + managedEmp.getAddress());
+            }
+            if (emp.getManagedEmployees() == null) {
+
+            }
+        }
+
+        assertEquals(13, getQuerySQLTracker(em).getTotalSQLSELECTCalls());
+
+        em.clear();
+        JpaHelper.getServerSession(getEMF()).getIdentityMapAccessor().initializeAllIdentityMaps();
+
+        q = em.createNativeQuery("SELECT e.EMP_ID, e.ADDR_ID, e.MANAGER_ID FROM EMPLOYEE e, SALARY s WHERE s.EMP_ID = e.EMP_ID ORDER BY e.EMP_ID");
+        List<Object[]> ids = q.getResultList();
+
+        assertEquals(14, getQuerySQLTracker(em).getTotalSQLSELECTCalls());
+        assertEquals(ems.size(), ids.size());
+
+        for (int index = 0; index < ems.size(); index++) {
+            Employee emp = ems.get(index);
+            Object[] idRow = ids.get(index);
+
+            assertEquals(emp.getId(), ((Number) idRow[0]).intValue());
+            if (idRow[2] != null) { // We have a manager
+                assertNotNull(emp.getAddress());
+                assertEquals("Incorrect address on: " + emp, emp.getAddress().getId(), ((Number) idRow[1]).intValue());
+            } else {
+
+            }
+        }
     }
 
     /**
diff --git a/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/test-src/test/fetchplan/FetchPlanExamplesTests.java b/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/test-src/test/fetchplan/FetchPlanExamplesTests.java
index 5985d63..b009635 100644
--- a/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/test-src/test/fetchplan/FetchPlanExamplesTests.java
+++ b/extensions/trunk/org.eclipse.persistence.example.jpa.fetchplan/test-src/test/fetchplan/FetchPlanExamplesTests.java
@@ -323,6 +323,54 @@
     }
 
     @Test
+    public void copyMergeExample_Clear() throws Exception {
+        EntityManager em = getEntityManager();
+
+        em.getTransaction().begin();
+        this.examples.copyMergeExample(em, true);
+
+        assertEquals(6, getQuerySQLTracker(em).getTotalSQLSELECTCalls());
+        assertEquals(0, getQuerySQLTracker(em).getTotalSQLINSERTCalls());
+        assertEquals(0, getQuerySQLTracker(em).getTotalSQLUPDATECalls());
+        assertEquals(0, getQuerySQLTracker(em).getTotalSQLDELETECalls());
+
+        try {
+            em.flush();
+
+            assertEquals(6, getQuerySQLTracker(em).getTotalSQLSELECTCalls());
+            assertEquals(0, getQuerySQLTracker(em).getTotalSQLINSERTCalls());
+            assertEquals(1, getQuerySQLTracker(em).getTotalSQLUPDATECalls());
+            assertEquals(0, getQuerySQLTracker(em).getTotalSQLDELETECalls());
+        } finally {
+            em.getTransaction().rollback();
+        }
+    }
+
+    @Test
+    public void copyMergeExample_NoClear() throws Exception {
+        EntityManager em = getEntityManager();
+
+        em.getTransaction().begin();
+        this.examples.copyMergeExample(em, false);
+
+        assertEquals(3, getQuerySQLTracker(em).getTotalSQLSELECTCalls());
+        assertEquals(0, getQuerySQLTracker(em).getTotalSQLINSERTCalls());
+        assertEquals(0, getQuerySQLTracker(em).getTotalSQLUPDATECalls());
+        assertEquals(0, getQuerySQLTracker(em).getTotalSQLDELETECalls());
+
+        try {
+            em.flush();
+
+            assertEquals(3, getQuerySQLTracker(em).getTotalSQLSELECTCalls());
+            assertEquals(0, getQuerySQLTracker(em).getTotalSQLINSERTCalls());
+            assertEquals(1, getQuerySQLTracker(em).getTotalSQLUPDATECalls());
+            assertEquals(0, getQuerySQLTracker(em).getTotalSQLDELETECalls());
+        } finally {
+            em.getTransaction().rollback();
+        }
+    }
+
+    @Test
     public void fetchCopyMergeExample() throws Exception {
         EntityManager em = getEntityManager();