I have been receiving this error a TON since using the PDF feature to annotate readings for school. It happens on the machine I did not upload the PDF to and typically requires I force sync the knowledge base on one or both machines to fix. Seems like the sync algorithm could use some adjustments for PDFs.
In this case, after I force synced the machine I did not upload the file on it worked. However, the rest of my materials did sync suggesting that the normal auto-sync just is not catching these PDFs.