One: running out of fuel. If they can't find or make more hypermatter in this new Galaxy, they're in trouble. At best they'll end up as just another local warlord, and the enemies their actions might have made in the meantime could lead to them getting dog piled at this point.
Two: the entire Borg collective. The Borg might not win, but firing several thousand turbolaser bolts will further deplete fuel reserves. How long can an ISD function without refueling if its routinely going into heavy combat situations? However, if we can indeed take Voyager's ending to mean that the Borg are destroyed, or at least crippled, this shouldn't be an issue.
Three: Subspace anomalies and the like. These things don't seem to be common in the Empire, but they're everywhere here. Surely the Empire will blunder into one they don't know how to get out of sooner or later?
Four: The Q. Voyage repeatedly encountered them. If Q decides to have some fun with the ISD...
Actually, I'd pay good money to see Q run circles around one of those stiff-necked, all-business Imperial officers.
