Having a VCS that stores changes as refactorings combined with an editor that reports the refactorings directly to the VCS, without plain text files as intermediate format, would avoid losing information on the way.

The downside is tight coupling between VCS and editor. It will be difficult to convince developers to use anything else than their favourite editor when they want to use your VCS.

I wonder if you can solve it the language-server way, so that each editor that supports refactoring through language-server would support the VCS.