HOFMAN There's nothing Skim can do about this, because you lose the notes when you save from another program. Skim has no way to change the way Preview or Acrobat saves data, that should be obvious. Remember, you also /see/ a PDF without (Skim) notes in Preview, so you should also expect to save it without notes when you do a save from Preview. That's /your/ fault, not Skim's. It's simple: save Skim data with Skim, and save Preview data with Preview. If you mix that up, you may expect problems.
(Version 1.3.1)