Just re-running the conversion seemed to work (although I did turn on the options to collapse forms and collapse senses, which probably made the difference). I've also re-done some of the changes SMK had made to the file which were documented in the <revisionDesc>. Some 11 or so entries will now be in the new version of the file which had previously been removed from the old, but these will get removed in due course later as we track down duplicates (or they'll be left at the end of the whole process, and be visibly superfluous).