AFAIK theres an issue with precompiling sites and the app_globalresources file (sorry, can't remember the details off the top of my head, but think it's to do with multiple languages). Changes were checked in to fix this a while back, but caused an issue, so were rolled back a few weeks ago. The issue was discussed in a corechat as well, so I believe a solution is being sought for it.

Cathal

I haven't had a chance to look at it, but i'm guessing you would have to keep a copy that was not precompiled, use it to do upgrades, and then precompile it (obviously, you'd use the same database connection details for both)

Cathal