I found the "check for new/found media" tool in the options menu but it didn't seem to help. I got frustrated with it this morning and deleted all files and cleared cache and data and then restarted the sync. I wasn't able to complete much, but it looks like what completed is valid. The album art used to be in a different folder and is now in the album path named "albumart.jpg" or similar. Although I won't need any suggestions at this point, it'll be nice when I run into this again (it will happen as sd doesn't last forever).

Duplicates and greyed out files is an issue in MMA? It probably still has the old copies in the Library. Have you initiated rescanning in MMA?

I had an issue with my SD card, so I copied the files to a replacement on my windows laptop. None of the media files worked correctly in MMA, so I deleted all files from the SD card in the 2 mediamonkey paths and the internal card. This didn't work as expected (files not found), so I deleted all media files and synced last night. All tracks and play lists appear to have been restored, but I have duplicate entries for every track (one gray, one usable), the play lists are broken, and the there is no album art. Other I can fresh install, delete all media, and start over but I don't have time before work to wait that long. Is there something that can be done to clean things rather than start anew?