Um yeah . . . the best thing to do is clean your savegame completely if you already have the original muffinwind. The update? Not really compatible with it's former self.
I use MCP and did the update with Wrye, but in the very first baker's tomb, there was doubling of doors, walls missing, and all the scripts were reset. I didn't try to clean all the cells out with EE; that might work better, but I think I'd rather start over and see all the great new muffin-ness from the beginning.
I'll let you know how that goes when I'm ready to start over.
Wait, what update are you playing here? I don't think anyone except Mireneye has the beta of the new version.
Anyway, if you've been through cells edited by a mod with a character already, updating it is very unlikely to go smoothly; however, cells you haven't yet visited should function fine. IIRC, you visit the Baker's tomb two or three times over the course of the mod, so doubling might be hard to avoid.