Try to use incremental resolution after removing overlays.

pkg/analyzer/lib/src/generated/engine.dart

 // Copyright (c) 2014, the Dart project authors.  Please see the AUTHORS file
 // for details. All rights reserved. Use of this source code is governed by a
 // BSD-style license that can be found in the LICENSE file.
 
 // This code was auto-generated, is not intended to be edited, and is subject to
 // significant change. Please see the README file for more information.
 
 library engine;
 
 import 'dart:async';
@@ skipping 2152 matching lines @@
 
   @override
   bool handleContentsChanged(
       Source source, String originalContents, String newContents, bool notify) {
     SourceEntry sourceEntry = _cache.get(source);
     if (sourceEntry == null) {
       return false;
     }
     bool changed = newContents != originalContents;
     if (newContents != null) {
-      if (newContents != originalContents) {
+      if (changed) {
         _incrementalAnalysisCache =
             IncrementalAnalysisCache.clear(_incrementalAnalysisCache, source);
         if (!analysisOptions.incremental ||
             !_tryPoorMansIncrementalResolution(source, newContents)) {
           _sourceChanged(source);
         }
         sourceEntry.modificationTime =
             _contentCache.getModificationStamp(source);
         sourceEntry.setValue(SourceEntry.CONTENT, newContents);
       } else {
         sourceEntry.modificationTime =
             _contentCache.getModificationStamp(source);
       }
     } else if (originalContents != null) {
       _incrementalAnalysisCache =
           IncrementalAnalysisCache.clear(_incrementalAnalysisCache, source);
-      changed = newContents != originalContents;
       // We are removing the overlay for the file, check if the file's
       // contents is the same as it was in the overlay.
       try {
         TimestampedData<String> fileContents = getContents(source);
         String fileContentsData = fileContents.data;
         if (fileContentsData == originalContents) {
           sourceEntry.setValue(SourceEntry.CONTENT, fileContentsData);
           sourceEntry.modificationTime = fileContents.modificationTime;
           changed = false;
         }
+        newContents = fileContentsData;
       } catch (e) {}
       // If not the same content (e.g. the file is being closed without save),
       // then force analysis.
       if (changed) {
-        _sourceChanged(source);
+        if (!analysisOptions.incremental ||
+            !_tryPoorMansIncrementalResolution(source, newContents)) {
+          _sourceChanged(source);
+        }
       }
     }
     if (notify && changed) {
       _onSourcesChangedController
           .add(new SourcesChangedEvent.changedContent(source, newContents));
     }
     return changed;
   }
 
   @override
@@ skipping 9624 matching lines @@
     PendingFuture pendingFuture =
         new PendingFuture<T>(_context, source, computeValue);
     if (!pendingFuture.evaluate(sourceEntry)) {
       _context._pendingFutureSources
           .putIfAbsent(source, () => <PendingFuture>[])
           .add(pendingFuture);
     }
     return pendingFuture.future;
   }
 }