If any of the segments post to the "wrong" account, it will be hard to reverse it. Airlines are careful about prevent double credit, and since the systems are not linked up between airlines, they tend to be pretty conservative (i.e. stingy) about it.

My advice: Call to change the FF# on your return segments after you fly the outbound. You can also change and/or double-check the new FF# at the gate on your return. A change at that point shouldn't affect already-flown segments. I can't swear this will work for all airline combinations, but it has worked for me with UA/US in the past.