I'd be willing to wager that the ships that defected will make an appearance. Chekhov's Gun demands it. I'm thinking the reason we haven't seen them is because either Adm. Byrne or the Fedayeen are in command of them as assets, otherwise I imagine they would have been a hell of thing to throw at the Carthage in Delenda Est and despite their rarity and importance, I think that Adm. Netreba and Adm. Calder would have committed at least one of them if they'd been able.
Using those ships in a decisive battle that concludes in the UEF's favor would have huge psychological impact on the GTVA, sort of like salt in the proverbial wounds. The UEF is in a bad way, but they don't necessarily need a total military victory. Psychological impact is gonna be a lot more important in part 3. On one side, you've got a brilliant but underhanded strategic and tactical genius whose exploits would pretty much cause the defecation to hit the ventilation if they ever got revealed. On the other side, you've got a despairing former flower-child civilization fighting like a cornered animal.
Whatever happens, this is gonna get REALLY interesting.