One Plus One CM12 update always reboots and starts the "Android is Upgrading..." process About my Phone:
It's a rooted One Plus One with twrp and CM12 installed.

I updated CM12 with a Update zip which had to be flashed manually through twrp. When i now want to boot the Phone it always starts "Android is Upgrading...". When the process is finished, the Phone reboots on it's own and runs through the same Process again and again.

Does anyone have an idea how stop this and boot normally?
Did you perform a full factory reset or did you do a "dirty flash"?

If it is the latter, make sure that you perform a full factory reset, including the cache, and then re-flash; that should solve your problem, it did for me at least.

If that doesn't work I reccommend using the latest build of BlissPop which is built on CM12.1 and runs like butter.