If you got the complete Hunter's set (and Ulthring's Leggings if you mindread Raze) and took out the 3 generators, then it sounds like you have completed everything. I flew around each flying fortress after defeating the boss to check for any stray chests or opponents I may have missed; unfortunately you can not check for ground opponents without switching to human form (which I did if I wasn't sure I recognized a particular location), but you can see if there are crates or barrels around from the air (break them as you explore and unbroken ones mark new territory), as well as whether chests are open or closed.
There is an achievement when you have taken out all of the flying fortresses, but nothing to confirm when you have cleared each individual one.
