Files are added with absolute URIs, but invalidated with file URIs.

pkg/front_end/lib/src/incremental_kernel_generator_impl.dart

 // Copyright (c) 2017, 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.
 
 import 'dart:async';
 import 'dart:io';
 
 import 'package:front_end/file_system.dart';
 import 'package:front_end/incremental_kernel_generator.dart';
 import 'package:front_end/src/base/api_signature.dart';
@@ skipping 259 matching lines @@
     saltBuilder.addInt(DATA_VERSION);
     saltBuilder.addBool(_options.strongMode);
     saltBuilder.addString(_entryPoint.toString());
     _salt = saltBuilder.toByteList();
   }
 
   /// Refresh all the invalidated files and update dependencies.
   Future<Null> _refreshInvalidatedFiles() async {
     await _logger.runAsync('Refresh invalidated files', () async {
       for (var fileUri in _invalidatedFiles) {
-        var file = await _fsState.getFile(fileUri);
-        await file.refresh();
+        var file = _fsState.getFileByFileUri(fileUri);
+        if (file != null) {
+          _logger.writeln('Refresh $fileUri');
+          await file.refresh();
+        }
       }
       _invalidatedFiles.clear();
     });
   }
 
   List<int> _writeProgramBytes(Program program, bool filter(Library library)) {
     ByteSink byteSink = new ByteSink();
     new LimitedBinaryPrinter(byteSink, filter).writeProgramFile(program);
     return byteSink.builder.takeBytes();
   }
@@ skipping 11 matching lines @@
   /// TODO(scheglov) Use API signatures.
   /// TODO(scheglov) Or use tree shaking and compute signatures of outlines.
   final String signature;
 
   /// Kernel libraries for libraries in the [cycle].  Bodies of dependencies
   /// are not included, but but references to those dependencies are included.
   final List<Library> kernelLibraries;
 
   _LibraryCycleResult(this.cycle, this.signature, this.kernelLibraries);
 }