how does "throw away duplicate" work?

I download a lot of articles from google scholar for my dissertation. I sometimes find myself downloading the same article multiple times; cluttering my computer.I tried my reference manager, Sente, to delete duplicates. But, Sente is not very efficient to detect duplicates. I want hazel to keep my mac clean from duplicates. Therefore, I was thinking to put my whole hard-drive as a folder into hazel and tick "throw away duplicates". My worry is it might delete the articles I read and annotated before. (I don't want hazel to delete older articles; I want it to delete the newly downloaded ones immediately as soon as they arrive in my Downloads folder).
is it safe to put my whole hard drive and ask hazel to throw away duplicates?
won't it delete the earlier ones (the ones I kept inside Sente folder)?
is it safe to put my whole hard drive and ask hazel to throw away duplicates?
won't it delete the earlier ones (the ones I kept inside Sente folder)?