2to3, svn rev 61623.  To reproduce this error:

$ cat <<! > foobar.py
# line 1
# line 2

from __future__ import with_statement
import sys
!
$ 2to3 -w foobar.py
RefactoringTool: Skipping implicit fixer: buffer
RefactoringTool: Skipping implicit fixer: idioms
RefactoringTool: Skipping implicit fixer: ws_comma
--- foobar.py (original)
+++ foobar.py (refactored)
@@ -1,5 +1,2 @@
-# line 1
-# line 2
 
-from __future__ import with_statement
 import sys
RefactoringTool: Files that were modified:
RefactoringTool: foobar.py
$ cat foobar.py

import sys
$