Hmm, as far as I know, FLEx doesn't currently try to import the morphemes and glosses.... But it sounds like you have had at least some success with that.
There was some work done internal to the program to implement that, but it wasn't taken to the point of actually working for users, as far as I know. Maybe you have discovered a way to access that!
One reason we have never made that possible is exactly the reason you state: What to do with entries that are already in the lexicon is challenging, especially if there is more than one piece of information about the morpheme, and some pieces match the lexicon but others don't.
We do hope to be able to do that kind of import some day, but it hasn't risen to the top of the priority list yet.
-Beth