Did you delete your JUKEBOX folder?
I just did a quick test and scratched The Movie data with a NFO file for. One Day (2011) URL from IMDB, however it was in the movie folder The Dilemma. I wanted this to happen.
It pulled everything for, One Day like it should. About, description, fanart, folder.
now i CHANGED the NFO file to the correct one, for the dilemma without deleting ANY files (not jukebox or existing about/folder.jpg) YAMJ scratched it, said the NFO was changed.
Interesting it just Changed the description, updated titles, directors, genre, starring, to the Dilemma AND changed the folder.jpg, however the actual fanart background and dvd folder in about.jpg remained from the original fake NFO i created to just put wrong files in there.
So, if I were to specify an NFO file, it will update everything except the fanart behind about.jpg, BUT the information will be correct! (it simply sees that there is a background for the title and uses it, without replacing)
I had to delete my jukebox folder and re-run YAMJ to have it compile the correct background (deleting about.jpg from the movie folder did not work!)
With this in mind, I actually have a Unscratched Folder & Scratched Folder. Whenever i start YAMJ2 Med8er, I have a batch file that DELETES my jukebox. SO it has a FRESH folder for every scan it does in the Unscratched Folder. That way less scans, faster results, just cut and paste finished folders so you know what is done and accurate!
IMO you do not need to scan your ENTIRE database, just new entries going into it or ones that need fixing, which should be separated from that database anyways as their values are incorrect.