Hmmm, you are in a tough position. Perhaps you can run 2to3 on a 2.6-fork and then merge the results of this into your 3.1 branch?
Alternatively, perhaps this pain will force you to rethink your strategy of maintaining two different branches for two versions of Python? I was lucky to use the same code base for both versions: Running the same code in Python 2.x and 3.x
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