My Conjecture:
Dunbarrow Cove: Discovered and raided. Or continues as a smugglers/pirate heaven.
Battlehorn Castle: Continues as a mercenary stronghold. Or is claimed by the legion for the war('s).
Frostcrag Spire: Odd it isn't visible from skyrim. Likely destroyed for some magical reason. Could be an oversight and it's now claimed by the synod or an independent group of mages. Given it's magical nature could it be "relocated" somewhere else?
Deepscorn Hollow: Likely a vampire heaven now. Or got ransacked by the KOTN(or some other Do-Goody faction).