When creating the folder /world_nether/ the data about nether fortresses is ignored. This moves the locations of nether fortresses, breaking existing wither skeleton farms and natural wither skeleton spawn in existing fortresses.

I think I've solved the problem. The solution is to copy the file Fortress.dat from /world/data/ to /world_nether/data/. Probably is also a good idea to copy villages_nether.dat and villages_end.dat to their respective locations for future proofing in case they are used in the future.