An update. I decided to try to restore from a backup since it rebuilds the database completely. Good news is this resolved the duplicate notes showing up in wiki link autocomplete suggestions. However, I still have the issue where some notes are never suggested that I mentioned here Wild inconsistencies between quick switcher, search and autocomplete - #8 by pk37.
A word of caution especially if you use @crumbletop’s method of linking to notes with their url. A restore from backup changes every note’s id. I link to a few notes in my reminders app with these url’s and had to redo them all since they had changed. Everything else with the restore worked flawlessly as far as I can tell.