I recently started using Zotero (+Zotfile), so please forgive my ignorance. Also, while writing this question I realised I am having a hard time describing the problem clearly, so please bear with me and ask for clarifications if anything is unclear.

I have a (small) collection with PDFs that I manually linked to Zotero. Initially everything looked fine, having 1 attachment for each parent item, but for some reasons the attachments are duplicating. See https://imgur.com/M9q8X1a for example: the publication by Rouet-Leduc et al is listed twice, and is now physically present in a subfolder as "[title].pdf" and "[title]2.pdf" ([title] refers to a long title of authors/year/publication title/etc). The publication by Valentine et al. (2013) is listed five times, two of which are physically present in a subfolder "[title].pdf" / "[title]2.pdf", and the other three are no longer found on the hard drive. There are other publications that don't have duplicates in the file subfolder (so no [title].pdf / [title]2.pdf), but still appear as duplicates attachments that can no longer be found. And there is one publication that has not been duplicated at all.

I haven't detected much systematics in this behaviour, and I cannot imagine that this is intended by the developers. I wonder if this behaviour will persist, creating more and more duplicates (and duplicates of duplicates, etc.), and I would like to know if there is a way of automatically cleaning up these duplicates. For my little test collection it wouldn't be a problem to do this manually, but for my main collection (comprising thousands of publications) it is practically impossible to do so.

In the end, I want to have the attachments of each Zotero collection in their own subfolder on my file system, and not buried in this terribly cluttered and obscure Zotero storage folder.

Again, apologies for the confusing problem descriptions.