This is a Virtuali addon manager issue. The issue isn't duplicate entries, it's that there is an old scenery that installed via the Virtuali addon manager, and a new scenery via the FlightBeam manager, and the Virtuali addon manager won't let me uninstall the old one.
The problem doesn't have anything to do with our Addon Manager, and it doesn't have anything to do with the different manager software used.
The issue is the OLD SFO was never updated to support the newer installation system outside the sim, because Flightbeam probably assumed most of its users would have updated to the much newer version anyway so, they never asked us to update the old SFO installer to the new one, the one that installs outside the sim.
However, in order to let *existing* user still using it, when we switched to the new installation system that installs outside the sim, our installer MOVED an existing SFO installation because, in order to continue working under the new folder, it had to stay together with all the other sceneries. This was the only way to let users of the old SFO to continue using it because, as I've said, there isn't a updated installer for it so, the other way (possible with all our sceneries and all the other Flightbeam sceneries), which was to uninstall, download the new installer and reinstall, wasn't possible with this one.
As explained in other threads, moving a scenery after it has been installer, results in the existing uninstaller to stop working because, Uninstallers are automatically created by their own installer, at installation time, creating a list of files that will have to be removed when uninstalling. But since we moved the scenery, this list won't work anymore. So, sceneries that were moved this way cannot be uninstalled automatically so, it must be removed manually.
If we didn't do that, and just required users to uninstall and download the new installers, this wouldn't been a problem but it would both required everybody to uninstall and redownload everything, just to move files AND it wouldn't work for those products that were never updated with the new system, like Flightbeam original SFO, and our own JFK V1.