diff --git a/build/org.eclipse.cdt.managedbuilder.core.tests/META-INF/MANIFEST.MF b/build/org.eclipse.cdt.managedbuilder.core.tests/META-INF/MANIFEST.MF
index 9d06cc0..ccd8ad9 100644
--- a/build/org.eclipse.cdt.managedbuilder.core.tests/META-INF/MANIFEST.MF
+++ b/build/org.eclipse.cdt.managedbuilder.core.tests/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %pluginName
 Bundle-SymbolicName: org.eclipse.cdt.managedbuilder.core.tests; singleton:=true
-Bundle-Version: 8.2.200.qualifier
+Bundle-Version: 8.2.300.qualifier
 Bundle-Activator: org.eclipse.cdt.managedbuilder.testplugin.CTestPlugin
 Bundle-Vendor: %providerName
 Bundle-Localization: plugin
diff --git a/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/regressions/Bug_580441Test.java b/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/regressions/Bug_580441Test.java
new file mode 100644
index 0000000..c5dbe8f
--- /dev/null
+++ b/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/regressions/Bug_580441Test.java
@@ -0,0 +1,70 @@
+/*******************************************************************************
+ * Copyright (c) 2011, 2022 Broadcom Corporation and others.
+ *
+ * This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License 2.0
+ * which accompanies this distribution, and is available at
+ * https://www.eclipse.org/legal/epl-2.0/
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ *
+ * Contributors:
+ *    Broadcom Corporation - Bug 303953 test
+ *    John Dallaway - Initial implementation (derived from bug 303953 test)
+ *******************************************************************************/
+package org.eclipse.cdt.managedbuilder.core.regressions;
+
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.io.ByteArrayInputStream;
+
+import org.eclipse.cdt.managedbuilder.testplugin.AbstractBuilderTest;
+import org.eclipse.core.resources.IBuildConfiguration;
+import org.eclipse.core.resources.IFolder;
+import org.eclipse.core.resources.IProject;
+import org.eclipse.core.resources.IWorkspaceRunnable;
+import org.eclipse.core.resources.IncrementalProjectBuilder;
+import org.eclipse.core.resources.ResourcesPlugin;
+import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.junit.jupiter.api.Test;
+
+/**
+ * Test that removal of a directory containing source file(s) is
+ * processed correctly by the default GnuMakefileGenerator.
+ */
+public class Bug_580441Test extends AbstractBuilderTest {
+
+	@Test
+	public void testBuildAfterPopulatedSourceFolderDelete() throws CoreException {
+		setWorkspace("regressions");
+		final IProject app = loadProject("helloworldC");
+
+		// Create additional source file at src/test/test.c
+		final IFolder testFolder = app.getFolder("src/test");
+		testFolder.create(false, false, null);
+		testFolder.getFile("test.c").create(new ByteArrayInputStream("int test;".getBytes()), false, null);
+
+		// Build debug configuration
+		setActiveConfigurationByName(app, "Debug");
+		buildConfig(app.getActiveBuildConfig());
+		assertTrue(app.getFile("Debug/src/test/test.o").exists(), "test.o not created");
+
+		// Delete folder containing test.c and build again
+		testFolder.delete(false, null);
+		buildConfig(app.getActiveBuildConfig());
+		assertFalse(app.getFolder("Debug/src/test").exists(), "test folder not deleted");
+	}
+
+	private void buildConfig(IBuildConfiguration config) throws CoreException {
+		ResourcesPlugin.getWorkspace().run(new IWorkspaceRunnable() {
+			@Override
+			public void run(IProgressMonitor monitor) throws CoreException {
+				ResourcesPlugin.getWorkspace().build(new IBuildConfiguration[] { config },
+						IncrementalProjectBuilder.INCREMENTAL_BUILD, true, monitor);
+			}
+		}, null);
+	}
+
+}
diff --git a/build/org.eclipse.cdt.managedbuilder.core/META-INF/MANIFEST.MF b/build/org.eclipse.cdt.managedbuilder.core/META-INF/MANIFEST.MF
index bb7707b..e83988e 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/META-INF/MANIFEST.MF
+++ b/build/org.eclipse.cdt.managedbuilder.core/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %pluginName
 Bundle-SymbolicName: org.eclipse.cdt.managedbuilder.core; singleton:=true
-Bundle-Version: 9.4.0.qualifier
+Bundle-Version: 9.4.100.qualifier
 Bundle-Activator: org.eclipse.cdt.managedbuilder.core.ManagedBuilderCorePlugin
 Bundle-Vendor: %providerName
 Bundle-Localization: plugin
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/makegen/gnu2/GnuMakefileGenerator.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/makegen/gnu2/GnuMakefileGenerator.java
index c1e3d3e..3275517 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/makegen/gnu2/GnuMakefileGenerator.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/makegen/gnu2/GnuMakefileGenerator.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2003, 2016 IBM Corporation and others.
+ * Copyright (c) 2003, 2022 IBM Corporation and others.
  *
  * This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License 2.0
@@ -17,6 +17,7 @@
  *     Marc-Andre Laperle
  *     Liviu Ionescu - [322168]
  *     Dorothea Pilz-Roeder (Advantest Europe GmbH) - [180451]
+ *     John Dallaway - [580441] fix processing on source folder deletion
  *******************************************************************************/
 package org.eclipse.cdt.managedbuilder.makegen.gnu2;
 
@@ -192,7 +193,9 @@
 							// This is a source file so just add its container
 							if (fo == null || fo.buildsFileType(ext)) {
 								generator.appendDeletedFile(resource);
-								generator.appendModifiedSubdirectory(resource);
+								if (resource.getParent().exists()) {
+									generator.appendModifiedSubdirectory(resource);
+								}
 							}
 						}
 						break;