It shouldn't delete your profile data unless you said "delete everything" when you uninstalled. If you did check that, then it's all gone (sorry). It's there so that if you're (say) selling your computer and uninstall firefox, you would expect that information not to persist.

I thought since I had two "instances", with what I thought were two profiles, It would just delete the beta version. So much for thinking 8^) Good thing I do nightly backups ...