On a single connecting trip, can I get one segment credited to one program and another segment credited to a partner's program?

This is for purposes of topping off accounts to get to redeemable balances.

I've used different programs for outbound and return, but not for different segments of the same one way trip.

My concern is that if I check in with program A, then change to program B at the connecting airport, that I will get program B for both segments when the computer does it's thing that night.

Is software complex enough to track FF info per segment?

In this case I'll be flying NWA.