Thanks for sharing, will try today to reproduce this. The problem sounds like it's the cache which is not erasing the folders from its memory (you can check this if you see a dup, go to Help > Reset Caches in the menubar).
update: I moved all files out of the folders in noteplan and deleted all folders in Finder. It's actually not so bad, frequently used files move back to the top once I change a little something, and the side bar contains a helpful history of what files I have been working on. For duplicates, I color tagged all files named " 2.md and " 3.md" and use the Compare feature in BBedit as I come across them. It would be Important to keep Noteplan forgiving with respect to changing files in the Finder, such as renaming, including the attachments folders.
Omg, this! I get duplicates all the time, but I always thought it was me being clumsy. I suddenly feel better if this is, in fact, a bug 😅
thanks! I can't check the cache fix right now, deleted all folders and since then, all duplicates I see are old, I clean them up as I find them.