MusicBee's duplicate manager can do the track comparison for you. My preference is to put the duplicates in a playlist and manually remove the ones I don't want. You can also copy tags/artwork from one track to another before deleting, that way.
For preserving artwork, look at the settings in Tags (1) preferences. I'm not sure if a rescan after changing storage settings is enough to trigger an export or not. There's also a Send To > Replace File function that will preserve tags and artwork, but it has to be done one track at a time.