diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/AbstractIndexerTask.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/AbstractIndexerTask.java
index 3974161d378..a2a01509eb6 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/AbstractIndexerTask.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/AbstractIndexerTask.java
@@ -626,12 +626,17 @@ public abstract class AbstractIndexerTask extends PDOMWriter {
 		}
 		
 		IIndexFileLocation[] ifls= orderedIFLs.toArray(new IIndexFileLocation[orderedIFLs.size()]);
-		addSymbols(ast, ifls, fIndex, 1, false, configHash, fTodoTaskUpdater, pm);
-		for (IIndexFileLocation ifl : ifls) {
-			info= getFileInfo(linkageID, ifl);
-			assert info != null;
-			if (info != null) {
-				info.fIsUpdated= true;
+		try {
+			addSymbols(ast, ifls, fIndex, 1, false, configHash, fTodoTaskUpdater, pm);
+		}
+		finally {
+			// mark as updated in any case, to avoid parsing files that caused an exception to be thrown.
+			for (IIndexFileLocation ifl : ifls) {
+				info= getFileInfo(linkageID, ifl);
+				assert info != null;
+				if (info != null) {
+					info.fIsUpdated= true;
+				}
 			}
 		}
 	}
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMWriter.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMWriter.java
index e5c195c6767..399a5096e78 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMWriter.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMWriter.java
@@ -8,7 +8,6 @@
  * Contributors:
  *    Markus Schorn - initial API and implementation
  *******************************************************************************/ 
-
 package org.eclipse.cdt.internal.core.pdom;
 
 import java.util.ArrayList;
@@ -199,11 +198,9 @@ abstract public class PDOMWriter {
 					} catch (RuntimeException e) {
 						stati.add(CCorePlugin.createStatus(
 								NLS.bind(Messages.PDOMWriter_errorWhileParsing, ifl.getURI().getPath()), e));
-						break;
 					} catch (PDOMNotImplementedError e) {
 						stati.add(CCorePlugin.createStatus(
 								NLS.bind(Messages.PDOMWriter_errorWhileParsing, ifl.getURI().getPath()), e));
-						break;
 					}
 					if (i<ifls.length-1) {
 						updateFileCount(0, 0, 1); // update header count