She could have survived a drop that trashed the Falcon.
I mean, all the characters on the first airship survived when it went down on the Second Continent.
Plus the Falcon was re-buildable, so it wasn't totally shredded.

Why wouldn't she try to get back? Who knows.
Maybe she got amnesia from a shot to the head during the crash.
Or maybe she went off in search of scattered parts for the Falcon, and Setzer found the wreckage and snatched it all up while she was gone, assuming she was dead somewhere.
Or maybe the ZoneEater found her and sucked her up (explaining how she got in the cave in the first place). No Daryl, scattered Airship parts everywhere...doesn't take much to assume "airship crashed and she's dead".

I don't think anyone will ever get definitive proof (Unless Square cracks and gives out a decent explanation, or somebody cracks the SNES game and finds something in the code that wasn't active in the game)