Yes the update in themes has always been like this, if i add some templates, settings, editing the exiting templates is No problem, but sometimes i need to delete a template maybe or deleting a setting, if i do that and you use upload a new version the deleted templates or setting will remain on your theme and does not get deleted.
open both of your theme settings in new tabs, the old one and the new version, copy paste the colors or any other changes you had, it wont take more than 5 minutes whats the big problem! :/