I doubt the Empire will like another civil war, not while the Time of Troubles is in living memory. Besides, I get the impression that Nikolaios and Andreas will drive Syria into the ground financially.
EDIT: Syrian tagmata rebelling is to be expected, given Nikolaios' proposal to cripple the Ottomans caters to their concerns & negates the land sales to Timur II. But I doubt any other tagmata will support the pretenders since, as I said, the Time of Troubles was only a generation or so ago and the Western units don't have as much rapport with Nikolaios & his desire to invade Mesopotamia.
Plus the pretenders won't have much leg to stand on. Since the Red Sea route has been cleared of hostile Muslims, shipping through Suez-Alexandria is much better for transporting goods in bulk, which in turn means the Silk Road won't generate all that much money. Add that to the fact that Syria is probably the poorest theme outside Coloneia you've got bankruptcy just waiting to happen, and when your army is paid in full cash this is a BAD thing. Perhaps Nikolaios & Andreas will attempt to revert back to the old Laskarid land grants + small cash method, but that'd piss off all the civilians they'd have to evict from the good farmlands.