** NOT SOLVED **...at least not for me.
World Update II: USA is installed and up-to-date on my system. If I delete FSDT Key West Intl in the content manager, Asobo's Fort Jefferson is definitely there (and, as expected, the docks, seaplane base, lighthouse, and other objects associated with your scenery are not).
When I reinstall FSDT Key West and return to the area
without restarting the sim, your objects are there; and the fort is there!
However,
after shutting down the sim and restarting, I notice that a Seaplane Base called KYW1 - Ft. Jefferson now appears on the World Map with a water runway (9-27) depicted to the northeast of the fort. Returning to the area, the fort is now
missing. Are you sure there may not be a stray exclude left over in your scenery (maybe associated with the seaplane base)? I bought my copy on the FS marketplace, showing v1.3.1 installed.