Great news Steve. Thanks.
My question is... if I turn off the "Store in file also" option and reapply the cover art to the files, will the cover art be removed from the file?
Change the option then, if the folder.jpg is still inside the album folder, just remove cover art from the files (Right click>Image>Remove) and then do a 'Quick Find in File / Cover Art Directory'. If Folder.jpg is not in the album folder and you have the image stored inside the file do the following:
1. Download and install King Sparta's plug in to 'Move to Folder.jpg'
2. Select track 1 on all affected albums and add to Playing now
3. Run the plugin to move art to folder.jpg
4. Select all affected albums and remove cover art but do not delete from hard drive.
5. Select all affected albums and do a 'Quick find...'