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TSRE5 needs a File "Save To" option.
Currently, you can only save your changed Route to the same File.
A "Save To" option would allow saving changes to a New Filename at any time.
So, a route project in-progress can have a saved file at various points in development

I don't think that's possible!
To save a route copy to another location all folders of the route have to be copied. But to load this route you also need the folders GLOBAL, SOUND and TRAINS.

Yeah, it'd have to copy everything over, while renaming certain files to the new name, perhaps even change some file entries. Not impossible, but possibly very time consuming to copy it all. Maybe a 'rename' function that just changes all required filenames/entries would probably work as well; You could copy your backup to another folder for safekeeping and then use the rename function to change the old or new name.