I see what you're getting at with the idea of starting with a clean sync file, and I love that you're tinkering around in the first place, because it's users in the community here that often figure out solutions. For example, we were all under the impression that it was not possible to restore a linked tree (because they forgot to add the feature into the backup tool) until a user here discovered the sync files. Then we all started making copies of our FTM files and those sync files, and we learned that we could move a linked tree from one computer to another without breaking the link.
Sorry, sync file. The only questions here are whether FTM creates a NEW sync file with the same name (since you renamed it) and if it OVERWRITES the old file. If FTM doesn't use the same name, then renaming the file doesn't accomplish anything. If FTM does use the same name, but replaces the old file, then renaming the file doesn't accomplish anything either.