Revenant folders on my Nexus 7 (flo) - how to track down the culprit?

This may have been going on for a while, but I have only noticed a few weeks ago. There are some folders **inside** the Downloads folder (i.e. subfolders and subsubfolders) which originally contained documents meant for a particular period and thus were named after year and month (e.g. 2014-05). They contained documents which I have read in apps like *Moon+ Reader*. I deleted those (sub)subfolders many times now, but they keep coming back. My first hunch was: "oh, somehow *Moon+ Reader* must have registered them in its DB and keeps recreating them". So I decided to use the rudimentary file browser included in that app and removed the folders there. Yet, after every reboot they keep reappearing. How can I track down the culprit? Is *Moon+ Reader* perhaps known to behave like that?