My Sim went to university and got a boyfriend, but left him behind when she finished her degree. I had her invite him to visit so that she could ask him to move in. I noticed that he had the option to confess to cheating to her, so I looked in his relationship panel to see who the other woman was. It was her, but a version from the University world.

I looked through the relationship-related options in Master Controller to see if I could somehow delete the other relationship, but she doesn't actually show up in the list of Sims. I suspect that this is because she is in the University world. To be honest, I'm kind of at a loss as to what else to try. Any ideas?

I imagine the breakup will be really rough.

Can you revert play to a save from before you invited the bf over and do this another way? Visiting sims from foreign worlds (Uni counts) arrive as low-data representations of themselves, also referred to as Mini-Sims. Asking a sim in that state to move in or marry has always been a risky proposition; the "real" sim is still back in their original world and what the game is doing is pulling just enough data from the TravelDB file to make it look like the real sim is visiting. This "other" relationship is a shadow, it doesn't sound real. Sometimes this works out anyway, sometimes not, but getting foreign sims to move in this way can also lead to game save corruption.

Although it's fine to have visitors if you send them back again, it's always a much safer bet to add a foreign world sim to your household by doing so in their world either by social interaction or by using MC > Add Sim, and then returning home with them. It's also safe to use MC to force the full version of a sim into your homeworld if they aren't already visiting by using NRaas > MC > Add Sim > Homeworld > (filter to the other sim's homeworld). You can add them to your household this way, a different one in town, or one of their own. If you have Overwatch, ErrorTrap, and Traveler in play, in that case the full duplicate of the arriving sim back in their own homeworld should get resolved soon enough, although possibly not until you visit that homeworld again so the game can simulate it properly.