This was a typo in the downgrade function for one of the patches. I
pushed a fix so if you update from bitbucket things should work smoothly
again (once we get to problem 2 below).

For anyone with galaxy-dist commit privileges, here's the one liner:

https://bitbucket.org/chapmanb/galaxy-central/commits/463852762a6eeadcf177312330ad1cd01053263d