I have noticed that every single time I log in to Mendeley Desktop (from my laptop or any of the Desktop computers I use (work + home)) duplicate files are created. Every time I want to download a paper I just throw it into one of the subfolders and voilá (I like this because papers often come with counter-productive titles, often with authoryear or author_year or whatever). I have configured Mendeley to use the 'Papers' folder as a watchfolder so every file I put in there gets synced to Mendeley.

I chose this setting because I can upload to Dropbox from any machine and I thought it could be a better idea than space provided by Mendeley (I still don't have a sound reason for this choice).

Inside that folder I have subfolders like 'Theme A', 'Theme B', 'Theme C' in order to get quicker access when I manually search for something. I have approximately 400 papers that weigh almost 380 MB, all of them stored in a Dropbox 'Papers' folder. I like it because of the reference manager and the multi-platform/OS.

I am using Mendeley for managing my papers.

Duplicate paper dropbox