searching for and deleting "flashfxp" should not mess anything else up since it's such a unique name there should not be any other application using that name
beside registry keys belonging to flashfxp itself, you might find a few MRU(most recently used) keys. it doesn't make much difference if you keep or delete them.
and as always, for safety, make backup of all the keys you are going to delete, in case you delete something you didn't mean to.