I have a large collection of music, sorted by album in individual folders, with relevant album art in each folder.

After I choose the "Reorganize Files and Folders" option, several folders remained in the source destination with the album art. The album covers appear in gmusicbrowser still. But they are orphaned, and now difficult for other programs to read.

Any suggestions on how to move this album art without doing it manually?

Sorry, there is no easy way to fix that.
I guess I could add a "move non-music files with the last music file of a folder" option, though it's not perfect and not as easy as it sounds (what about sub-folders, you have to check if they contain music, if there is a whole sub-tree that becomes messy)

I experienced the same behaviour and was about to ask for a way to fix this...

If You say it's difficult to move the other files as well, what about just renaming the whole folder? Still this could bedome messy when having "sub-trees", but , at least for me. that's hardly the case...