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

pkg/front_end/lib/src/incremental_kernel_generator_impl.dart

Index: pkg/front_end/lib/src/incremental_kernel_generator_impl.dart
diff --git a/pkg/front_end/lib/src/incremental_kernel_generator_impl.dart b/pkg/front_end/lib/src/incremental_kernel_generator_impl.dart
index 8c7f17ba7004d7e57ef3538564a076c07625000a..578f9b1c6b7acb27e527ed4386f0c8c78ed7dc98 100644
--- a/pkg/front_end/lib/src/incremental_kernel_generator_impl.dart
+++ b/pkg/front_end/lib/src/incremental_kernel_generator_impl.dart
@@ -277,8 +277,11 @@ class IncrementalKernelGeneratorImpl implements IncrementalKernelGenerator {
   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();
     });