Sorry to read that you went through this issue. It's weird. As far as I'm concerned, I didn't have any server error at all when updating from 12.0.1 to 12.1.0. The update went smoothly. First i updated to the Beta version (12.1.0-B1), later to the Final version (12.1.0) when it was released. (I have both 'Enable auto-update' and 'Force auto-update' set to Off)