I had the same problem. I found a slight syntax problem in the recommended cure:

Recommended - Search: formats:false {note: "formats"]

Did NOT work as I wished, showing me one entry out of two thousand plus known problem folders.

Search: format:false

Did work, showing me 2033 problem folders which I deleted.

I have no idea what was unique about the first try.

NOTE: In case some one else gets into the same mess I did, here's what happened to me and what I did.

I was ADDING large groups of documents to the new Calibre library. One group turned out to be an old backup, duplicating about 2000 documents with slightly different names since there was a change in our standard naming format some time back. I made a copy of the entire Calibre folder to experiment on then used a free util called FindAllDuplicates which calculates a unique "check sum" for each document then compares all documents, 11,544 in this case. The utility permits you to auto delete either the first or last item in each pair/group. This deleted my duplicate documents in the folder but left them in the Calibre database.

I used the procedure recommended in this thread to purge them from the database.

Thanks to all the "helpers"!