Same problem here.
A database with a new nation I had made over Crimea didn't have any problem with European qualification of any sort, but because I couldn't have a proper national team or produce regens from said nation, I decided to do it over, this time replacing Ireland Pre-1922. And this problem happened.
I tried feeding the Europa League some preset teams for the infamous stage 3 but it didn't work either (or I didn't do it the right way).
If anyone has a solution, I'm all ears...