At which point you need to run 2to3 again, and maybe update callers of the code you stashed, depending on what it actually does. If you know with certainty it isn't going to be affected in any way by the upgrade tool, of course, then either works as well. But otherwise I'd argue strongly for finishing the changes first, committing them, and only then running the upgrader.

It's an argument of preference in practice, and therefore all but guaranteed to go nowhere. I tend to think that updating a whole codebase like this is best done atomically rather than piecemeal, especially when the code belongs to a team rather than an individual. But I can see where opinions might differ on such a point.