How's this... They use a "psuedo" hive mind process for fleet coordination. Now you have two such "coordinators" in theater. The first one survived the great war and has been hiding out, the second one is from FS2 new fleet. They join up and the second one basically blows off the battle tested one proceeds to make the same tactical mistakes and assumptions the first one did (they don't get along and there is a pride thing going on also).
So long story short you can set up why/how this Shivan coordinator can rally his loyal troops and get the hell out of dodge and actually try to approach teh GTVA for whatever reason (honor of a victorious enemy, some greater understanding that maybe they MIGHT get along in the future with such a worthy warrior race, or maybe they NEED the help of the GTVA for something unknown to us for now...)
Whatever..
Just some ideas I threw out to ya...