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missing annotations

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I am using Mendeley Desktop and iPad and editing on both platforms. I noticed in different points that the annotations on the iPad are missing, and this is caused when the pdfs are "unloaded" (I don't know how this happens). If I re-download the pdf then the annotations are not displayed. I have sunch'ed the app but still nothing. I am afraid now that if I synch the desktop version the annotations will be lost for good. Can you please provide some advice, because this is days work that I am talking and would hate to lose them again! Thanks.

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