When the file content is the same as the being removed overlay contents, ignore the change.

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:math" as math;
@@ skipping 3197 matching lines @@
       } else {
         SourceEntry sourceEntry = _cache.get(source);
         if (sourceEntry != null) {
           sourceEntry.modificationTime =
               _contentCache.getModificationStamp(source);
         }
       }
     } else if (originalContents != null) {
       _incrementalAnalysisCache =
           IncrementalAnalysisCache.clear(_incrementalAnalysisCache, source);
-      _sourceChanged(source);
       changed = true;
+      // We are removing the overlay for the file, check if the file's
+      // contents is the same as it was in the overlay.
+      SourceEntry sourceEntry = _cache.get(source);
+      if (sourceEntry != null) {
+        try {
+          TimestampedData<String> fileContents = getContents(source);
+          String fileContentsData = fileContents.data;
+          if (fileContentsData == originalContents) {
+            sourceEntry.modificationTime = fileContents.modificationTime;
+            sourceEntry.setValue(SourceEntry.CONTENT, fileContentsData);
+            changed = false;
+          }
+        } catch (e) {
+        }
+      }
+      // If not the same content (e.g. the file is being closed without save),
+      // then force analysis.
+      if (changed) {
+        _sourceChanged(source);
+      }
     }
     return changed;
   }
 
   /**
    * Create a [GenerateDartErrorsTask] for the given source, marking the verification errors
    * as being in-process. The compilation unit and the library can be the same if the compilation
    * unit is the defining compilation unit of the library.
    *
    * @param unitSource the source for the compilation unit to be verified
@@ skipping 8972 matching lines @@
     if (element.id == _id) {
       result = element;
       throw new _ElementByIdFinderException();
     }
     super.visitElement(element);
   }
 }
 
 class _ElementByIdFinderException {
 }