Yeah the logic definitely needs some revamping to make it less destructive. Maybe some toggles in the settings, or commands you have to manually run to “start syncing”.
When you open a file, it doesn’t rewrite the filename, just the heading of that file. Only if you were to update that heading it would rename the file, but even for me it messed up some headings that I created before using this plugin 
I want to add some kind of tag to the file to mark it as “this is enabled for syncing” but don’t want to insert random stuff into documents