(I know the idea of a delete file button has been rejected.)

Sometimes when I have a disc with duplicates, I use my file manager to remove the duplicates, but there's no way to make the disc gold in Picard without manually removing the duplicate file entries.

My suggestion: make the Refresh option in the disc right click menu check that the file for the track entry still exists on disk, and, if it doesn't, remove the entry.

(Of course, one can, after deleting the duplicate files, just click Save on the disc, but you have to hope that removing the duplicates was the only thing to fix before Saving.)