I've observed what looks like a bug with the DeleteAirport, specifically the deleteAllJetways flag, but it's possible other flags in the DeleteAirport might be affected too.
If a replacement airport that has custom Jetways in the Community folder replaces a standard default airport with no "handcrafted" version, everything works as expected: the new airport can use the deleteAllJetways flag, and its custom jetways will show with no issues.
If the airport to be replaced has an "handcrafted" version in the Official folder ( doesn't matter if it's encrypted, like KSFO or not, like KJFK or KDFW ) which ALSO use the deleteAllJetways flag itself so, basically, we already have two versions of the airport and are adding a 3rd, the deleteAllJetways flag works only the first time the new airport is added. On every subsequent session of the sim, the replacement jetways which showed up the first time, can't be seen anymore. The Console doesn't report any problems, and confirms the add-on package has been loaded successfully in all sessions.
The problem can be fixed by manually removing the CONTENT.XML. As soon the file is removed to be regenerated, the new jetways shows up, but only for that first session. It's possible to go back to the Main menu, choose another airport, go back there and jetways are still showing. Everything works, provided the simulator is not closed. On the next session, the new jetways are not loaded, so a new cycle begins, requiring removing the CONTENT.XML again, which always fix the problem.
It doesn't seem a scenery priority problem. In all cases, the CONTENT.XML always had the new airport in the last line. There are no other add-ons in the Community folder and, when the CONTENT.XML is regenerated, the new one is byte-by-byte identical to the previous one that didn't work after the first time.
Removing the SceneryIndexes folder doesn't seem to make any difference, and it doesn't seem to change if *only* the CONTENT.XML is recreated, as long the installed packages are the same. The one and only thing that always solves the problem is removing the CONTENT.XML, which fixes the issue, but just for one session.
It seems the loading order works differently on a session where a CONTENT.XML is being recreated from scratch, compared to a session in which it was already present.
Another thing that fixes the issue, is manually editing the 2nd "handcrafted" .BGL, to unset the deleteAllJetways at the binary level, making the new replacement file the only .BGL that replaces jetways on that airport, which falls back in the first case, where everything's working if only one .BGL use the deleteAllJetways flag, which is the usual situation of default airports with no enhanced version.
I even tried replacing the entire airport, basically creating a clone of the default airport, with every element present ( taxiways, parkings, runways, ils, jetways, frequencies ) and the behaviour is still the same: custom jetways still don't show, except for the first session when a new CONTENT.XML is created, but not in subsequent sessions.