When it's done, the baggage train goes away, usually to its parking vehicle spot, or another parking if there isn't one. It can't obviously go to the terminal, since the AFCAD doesn't have the concept of a "terminal drop point for baggage", unless the AFCAD designer puts a vehicle parking spot in a location that might be suitable for that.
Of course, if the AFCAD has been badly designed, with unconnected nodes or parkings that are not reachable, the vehicles will have troubles, but that would create lots of other issues, even if GSX wasn't involved.