AFCI does have some ground fault protection, so you may be correct about the shared neutral.
Not sure about the best way, but turn everything off except the AFCI circuit, disconnect it's neutral and load the circuit. Not on the AFCI breaker, of course. Then use an ammeter to find the other neutral. Next, turn the other circuits on until you find the other hot using that neutral.
If it's K&T pull both circuits out of the panel and put them in one box and feed them with the AFCI circuit. Since K&T doesn't follow the rule about all conductors of a circuit in one cable, you should be able to abandon one neutral.
If it isn't K&T, the crossed neutrals will be in an accessable box, right? Then you could fix it the proper way.
Around here, we can change panels without taking responsibility for every plug in the house. You have my sympathy.
