You will most likely still have to do this manually, but if you do it once you have the site completed and are sure you won’t need anything you remove (or at least copy what you remove to a backup file so you know what’s missing) then you can just put the new file on the server and don’t replace it with the exported one on future uploads. Not too difficult to handle. Keep a copy of the new file as well just in case you accidentally overwrite it lol. Keeps it simple this way without having to deal with export scripts and such.
Just open the CSS file and upload the other files when you upload and don’t upload the min file and you’ll be good to go.