Okay, after the latest update I tried everything again and now the extracting and repacking finally works for my european version, but I modifying the game doesn't work. I tried to open Captain Falcon's moveset and parsed the animations, and everything was working fine. Just as a test I opened his forward aerial and modified the knockback a bit, closed it, saved it and then repacked everything. Then I started the game with HANS normally (EUR/DE) and tested if the change worked, but suddenly all of Falcon's moves had no hitbox anymore and his up and down smash froze the game. After that I tried to start the game in USA/EN and all of the moves got their hitboxes back but the knee, with was the only one I changed.
A few things that I noticed were that strangely the patched version had exactly the same file size as the unaltered original file and that patching a data(us_en) folder together with just the data folder didn't seem to change the result in any way.
I would appreciate any help, I have no idea what to do now...