Do replay files require consistency or can you spawn new units from the ether as required? I think you could get a system that would get the broad strokes unit placement correct, but having a shot-for-shot perfect replication seems impossible.
I was wondering how you could possibly sync up something like a Carrier that has multiple fighters.
Same way as everything else - you play out the simulation and see what happens. The behavior of the interceptors is as deterministic as any other unit. (They just happen to not be directly commandable by their owner.)