This is very closely related to the issues discussed in Format pages-metadata.edn before saving.
FWIW, I have stomped on versions of this file by simply picking one version in a Git merge and never had any problems. As we discuss in that linked suggestion, however, there is no way to reliably get that creation / modification info back. This will presumably mess up things like your recent pages list, etc. But your notes all keep working AFAICT.