Micro SD gets corrupted after every restart
The Solution was simple after all, chkdsk told me the volume was fine when I did a (basic) error check [/f] but when I did a check for bad sectors [/r] it found tons of errors and repaired them. It took some time but now I have all my data back!

So if you have this problem with any sd card mounted for example as drive u:\ then run in cmd:

chkdsk u: /r /v


ps: format my card as fat32 was no option as it is 128GB and I would lose all my data.