Here's something interesting for you. I managed to fix this problem finally a few days ago by getting rid of a plugin called "Simple Backup" ... It wasn't Yoast SEO after all. I only figured this out after restoring a backup to a few days ago when everything was working and then seeing the issue come back and THEN realizing that I had just installed the "Simple Backup" plugin that morning. So I got rid of it and no more messing with my .htaccess. So I think in all cases this must be an issue of misconfigured or crappily made plugins... I'm going with crappily made for Simple Backup since I didn't even do any adjustments to settings or anything, just right out of the box, as soon as it was installed the issue arised.
Hope this helps for you and anyone else that finds this thread.