There are a lot of silent pitfalls like that in my experience. For example, if you use folder level encryption with Synology Active Backup for MS365 it can silently mangle the file names due to path length restrictions. You'll end up with files that have "file name too long" as part of the file name.
That's why I'm trying to reconcile every file in this data set. I don't trust anything without being able to personally verify it at this point.