"I already change them so significantly they barely resemble the original"

You should ALWAYS make a copy and them modify the copy, otherwise you will LOSE all your changes if you ever upgrade the module to a new version

"and as I understand it this cannot be done"

no, it can be done right now.
/DesktopModules/Repository/Templates/My1stTemplate
/DesktopModules/Repository/Templates/My2ndTemplate

each template can have different text on the Upload button, so you can have 1 repository using My1stTemplate and a second repository using My2ndTemplate and they would have different text on the Upload button.

"Would I have to hide the module temporarily from them with a message saying 'Photo gallery being upgraded' and then just re-ftp the customised css/html files across to the server"

If you follow the above example, and then upgraded the repository module from 3.01.15 to 3.01.16, your users would never know since you are not using the standard template you are using custom templates, the upgrade only updates the module code and standard templates. I does not touch any custom templates that create. So your repositories would not change and your users will be unaffected. You would NOT need to re-ftp any custom files or html

Thanks Steve, this is probably something I should have taught myself a few months ago. Whoops.