have you been able to import your conference into the game at all? My import process with 16 teams crashes, times out...
to answer your question, in theory, you should be able to set the rivalries for your TB in the creation process on the TB site, using THE NORMAL UNIVERSITIES as the target... EXAMPLE:
you're replacing Michigan with TB Team #1, and you want to have a rivalry with TB Team #2, but they've replaced UCLA.
Go to TB site and sign in. Click on EDIT TB Team #1, go to the PROGRAM tab and make up the rivalry with UCLA. I'm not sure if you have to set the rivalry in reverse, ie, do the same process for TB Team #2, making the rivalry with Michigan... I've yet to even get the 16 team import process to pop off, yet... buggy crap
Do NOT accept this as an answer... make the mods work a little...