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Having the pdf and epub formats on your reader at the same time is only a problem with public library books. Otherwise, its not usually a problem. I am guessing that you are using sony's reader library software. If so, what you can do is make a collection for your pdf's and another for your epubs. Then go in to the sync button, uncheck all the boxes and then check only the collection that you want to sync. That should do it.
The other option is not to synch at all and drag and drop the books onto your reader instead.
Hope this helps.
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