Today I discovered, that wordpress automatically overwrites changes that I made to my .htaccess file. I don’t know since when this happens, but I assume since the last WordPress Update. Whenever I replace the file with my working backup, it gets overwritten within 2 minutes. I think, I now have a working way to prevent wordpress from doing so, the fix can be found here (for anyone who is interested):
I hope the site will now work as intended, sorry again for this!