If you're sure the preview showed correctly, but the files didn't move, I would have to guess permissions error.
A couple of other thoughts:
Did you leave the directories section active (checked) when you removed the base path entry? I wouldn't do that...
Did the files move elsewhere other than intended, or were they deleted, or did they remain in place but MC lost track of them? You need to clarify that.
Couldn't say much more without screenshots or a video.
For this type of operation though, what I would do is segregate my files in a view, by whatever criteria, then select the target files and use RMCF to do a search and replace on the filename, with the oher sections disabled. Especially if I were doing a lot of files, I wouldn't want to do too many different things at once. For example, I would break moving them to a different NAS vs restructuring names by tags into two steps.