Revenant folders on my Nexus 7 (flo) - how to track down the culprit?
I have now been able to confirm without doubt that indeed Moon+ Reader is responsible for the folders reappearing after deletion.

The problem is that I've come up empty-handed when looking for a database or text file related to Moon+ Reader which contains the names of those folders.

Meanwhile I have moved my books into the Books folder instead of leaving it in a subfolder of Download, but now the whole folder hierarchy inside Download which was used by Moon+ Reader keeps reappearing.

Unfortunately even rating the app requires a Google+ account which I will not create and there is no support contact given. So no way to report this issue back. But I am thinking about extracting the app and trying to find the offending code to add more details here.