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syncing and lost pdfs

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Hi, I use mendeley on thin clients so I have to install it everyday. I do not synchronize all the library and just download those files that I need; however, after downloading a file and doing highlights and taking notes and then synchronizing again I lose the pdf: the next day when I install Mendeley again the file is gone. I know my case is not standard but I am wondering what is the point of selective synching?

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