No profiles are automatically added to the tree from your GEDCOM through the GEDCOMpare process; likewise, matched profiles are not automatically edited either.
You have to process all the profiles (match or reject?) in your GEDCOM (or that appear in the popup processing window?) before you can add new profiles. Unprocessed profiles will remain so until you process them.
New profiles are only created when you add them; existing profiles are only edited when you edit them.
No profiles are removed from your GEDCOM via GEDCOMpare. Your uploaded file remains intact until you delete it or until the file is automatically deleted due to inactivity relevant to the file/ GEDCOMpare allows you to copy the information to WikiTree profiles, but does not alter your GEDCOM file.
You will be made the profile manager for any profiles you add, so they will appear on your Watchlist. You can orphan open profiles any time you so choose. You will not be added to the trusted list for profiles you edit; you will remain on the trusted list if you were already there.
The data in you uploaded GEDCOM remains available for 60 days (or longer - we seem to have a bug in the deletion function) after your last edit (or access?) from your GEDCOM via GEDCOMpare.
I think I covered most of your questions (and hopefully my information is reasonably accurate!). Post back if you have more questions, Carole.