That seems like a pretty big oversight on Konami's part. Why would we want to update a league of fake teams and players?
No idea!
After loading up the game for the first time I did the transfer update, then installed the OF.
Everything looked fine Bundesliga-wise till I started an exhibition match. The 4 German clubs who originally are in ''Other European Clubs'' went back there, the PEU League went from 18 to 20 clubs again and the 4 fake clubs I removed were back in too.
I still see Bayern, Wolfsburg etc. with the correct kits, emblem etc. but their squad is back to the original PEU League squad.
When I turn off the live update everything goes back to how it was after installing the OF.