So I can blithely restore docs.checksum from a backup without screwing up my Scrivener Project then?
Plus my context is to the OP’s mention of

‘Merge’ attempts to merge changes of the packaged files.
So I can blithely restore docs.checksum from a backup without screwing up my Scrivener Project then?
Plus my context is to the OP’s mention of
‘Merge’ attempts to merge changes of the packaged files.
I think I see the point of confusion, you’re talking about something completely different. If you are restoring the whole project from your backup, intact, every file exactly as it was saved when it was backed up, then your scenario wouldn’t come up.
The point of discussion is taking full user folder backups and getting the backup software’s settings tuned to work best with Scrivener. The goal is to have the whole project backed up exactly how it was on the working disk, down to the byte. Copying it back (restoring) in the other direction to an empty folder or whatever just makes another exact copy of it, and is no more or less risky than backing it up.
That aside, even if you did for whatever reason decide to only restore the docs.checksum file all by itself, maybe just to see what would happen, nothing bad would happen. It would at most merely trip the failsafe that would trigger a search index rebuild on next launch. That’s all that file does.
Merging isn’t relevant. We already discarded that as an option quite a ways back. It’s probably only a setting you would rarely want to use, for something perhaps like Obsidian that allows freeform text file storage (not that it hides its data vault behind a package though, to my knowledge, I just mean to use that kind of program as an illustration).