diff --git a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CConfigurationSpecSettings.java b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CConfigurationSpecSettings.java
index 1bc36162d44..7b0dc6c2740 100644
--- a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CConfigurationSpecSettings.java
+++ b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CConfigurationSpecSettings.java
@@ -657,43 +657,24 @@ public class CConfigurationSpecSettings implements ICSettingsStorage{
 	}
 
 	public void remove(ICConfigExtensionReference ext) throws CoreException {
-//		boolean fireEvent = false;
-//		synchronized (this) {
-			CConfigExtensionReference extensions[] = (CConfigExtensionReference[])getExtMap().get(ext.getExtensionPoint());
-			for (int i = 0; i < extensions.length; i++) {
-				if (extensions[i] == ext) {
-//					System.arraycopy(extensions, i, extensions, i + 1, extensions.length - 1 - i);
-					System.arraycopy(extensions, i + 1, extensions, i, extensions.length - 1 - i);
-					if (extensions.length > 1) {
-						CConfigExtensionReference[] newExtensions = new CConfigExtensionReference[extensions.length - 1];
-						System.arraycopy(extensions, 0, newExtensions, 0, newExtensions.length);
-						getExtMap().put(ext.getExtensionPoint(), newExtensions);
-					} else {
-						getExtMap().remove(ext.getExtensionPoint());
-					}
-//					updateOnDisk();
-//					if (!isInitializing) {
-//						fireEvent = true;
-//					}
-				}
-			}
-//		}
-//		if (fireEvent) {
-//			fManager.fireEvent(new CDescriptorEvent(this, CDescriptorEvent.CDTPROJECT_CHANGED, CDescriptorEvent.EXTENSION_CHANGED));
-//		}
+		doRemove(ext);
+		
+		fIsModified = true;
 	}
 
-	private void doRemove(String extensionPoint) throws CoreException {
+	private boolean doRemove(String extensionPoint) throws CoreException {
 //		boolean fireEvent = false;
 //		synchronized (this) {
 			CConfigExtensionReference extensions[] = (CConfigExtensionReference[])getExtMap().get(extensionPoint);
 			if (extensions != null) {
 				getExtMap().remove(extensionPoint);
+				return true;
 //				updateOnDisk();
 //				if (!isInitializing) {
 //					fireEvent = true;
 //				}
 			}
+			return false;
 //		}
 //		if (fireEvent) {
 //			fManager.fireEvent(new CDescriptorEvent(this, CDescriptorEvent.CDTPROJECT_CHANGED, CDescriptorEvent.EXTENSION_CHANGED));
@@ -702,9 +683,12 @@ public class CConfigurationSpecSettings implements ICSettingsStorage{
 
 	public void remove(String extensionPoint) throws CoreException {
 		
-		doRemove(extensionPoint);
+		boolean changed = doRemove(extensionPoint);
 		
 		checkReconsile(extensionPoint, false);
+		
+		if(changed)
+			fIsModified = true;
 	}
 
 	CExtensionInfo getInfo(CConfigExtensionReference cProjectExtension) {
@@ -891,4 +875,29 @@ public class CConfigurationSpecSettings implements ICSettingsStorage{
 		}
 		return refsMap;
 	}
+	
+	boolean extRefSettingsEqual(CConfigurationSpecSettings other){
+		if(fExtMap == null || fExtMap.size() == 0)
+			return other.fExtMap == null || other.fExtMap.size() == 0;
+		if(other.fExtMap == null || other.fExtMap.size() == 0)
+			return false;
+		
+		if(fExtMap.size() != other.fExtMap.size())
+			return false;
+		
+		for(Iterator iter = fExtMap.entrySet().iterator(); iter.hasNext();){
+			Map.Entry entry = (Map.Entry)iter.next();
+			ICConfigExtensionReference[] thisRefs = (ICConfigExtensionReference[])entry.getValue();
+			ICConfigExtensionReference[] otherRefs = (ICConfigExtensionReference[])other.fExtMap.get(entry.getKey());
+			if(thisRefs.length != otherRefs.length)
+				return false;
+			
+			Map map = createRefMap(thisRefs);
+			map.entrySet().removeAll(createRefMap(otherRefs).entrySet());
+			if(map.size() != 0)
+				return false;
+		}
+		
+		return true;
+	}
 }
diff --git a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionManager.java b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionManager.java
index 1b61f72cb60..4d849212e4c 100644
--- a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionManager.java
+++ b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionManager.java
@@ -1962,7 +1962,8 @@ public class CProjectDescriptionManager {
 
 	public CProjectDescriptionDelta createDelta(ICConfigurationDescription newCfg, ICConfigurationDescription oldCfg){
 		CProjectDescriptionDelta delta = new CProjectDescriptionDelta(newCfg, oldCfg);
-		
+		IInternalCCfgInfo newInfo = (IInternalCCfgInfo)newCfg;
+		IInternalCCfgInfo oldInfo = (IInternalCCfgInfo)oldCfg;
 		if(delta.getDeltaKind() == ICDescriptionDelta.CHANGED){
 			ICFolderDescription[] foDess = newCfg.getFolderDescriptions();
 			for(int i = 0; i < foDess.length; i++){
@@ -2057,6 +2058,16 @@ public class CProjectDescriptionManager {
 				}
 			}
 			
+			try {
+				CConfigurationSpecSettings newSettings = newInfo.getSpecSettings();
+				CConfigurationSpecSettings oldSettings = oldInfo.getSpecSettings();
+				if(!newSettings.extRefSettingsEqual(oldSettings))
+					delta.addChangeFlags(ICDescriptionDelta.EXT_REF);
+			} catch (CoreException e){
+				CCorePlugin.log(e);
+			}
+
+			
 			ExternalSettingsManager.getInstance().calculateCfgExtSettingsDelta(delta);
 			
 			int drFlags = calculateDescriptorFlags(newCfg, oldCfg);