[ownedbycats]

My filename template is {#kobopath}/{author_sort}/{title} - {authors}.

#kobopath is a fixed-value column with a few options (Fiction, Nonfiction, and Fanfiction essentially) just as a kludge to avoid cluttering up the root of the drive with a million author folders. It never changes once it's set.

I forgot to mention that the duplicate book appears in Calibre device view. Usually I notice it when SmartEject tells me there's duplicate books. I've never actually checked to see if it appears on the device itself because I just delete the old version.

I also have KoboTouchExtended set to treat it as a new book. I was thinking that if the book uploaded first, and then Kobo Utilities grabs the bookmark from the old version, Calibre sees it as two separate database entries. (It would also explain why it only happens sometimes - it depends on whether the bookmark or reading list sync happens first.) But that's kind of grasping at things.