Steps per mm of extruder are incorrect after rebuilding
Ok, thanks everyone for at least taking time to read or thinking about this.

The Problem is an absolute mess and there are two possible reasons:

-> the octoprint eeprom editor is broken

-> the ATMega2560's eeprom is broken. as far as i know companies buy used atmegas to cheapen the price and the >100k writes on my chip has been reached

I will try to figure out the exact problem, if i find time in the next days.
My current setup is just deactivate eeprom and i'm good to go. Even wiping eeprom with a small arduino sketch will get the error to return.

Now i will be able to sleep again :D