Obviously, the ones who don't want to participate just go off and do their own thing in the normal RP. You don't have to scrap cannon because of it. Those that go off onto the crossover will obviously be unavailable for the time the crossover is running. Or, you could say that it takes place in the future after each of the RP's finish, or something, which would mean you didn't have to scrap cannon, and both parties could still participate in both RPs if they wanted too.

[quote=Azathoth]
And inevitably people would get butthurt that their side didn't always win.
[/quote]

That's what the banhammer is for. And the GM's job, so I don't worry about that xP