This happened to me before while using Evernote installed on my Chromebook, which I only use occasionally. I thought it was user error -- that I had somehow accidentally deleted the PDF attachments -- but today it happened again under circumstances that I'm convinced was not user error. I had a note from back in March I was editing with 3 PDF attachments. I viewed one of the attachments, backed out to make a text edit in the note, and then suddenly 2 of the attachments suddenly disappeared. And then when I backed out, the Note itself had entirely disappeared. When I went to my phone's Evernote, I was able to pull up the note, still showing a thumbnail of one of the 2 deleted attachments, but still with 2 of the 3 attachments deleted. I went back to my Chromebook, ran the search again, and the note reappeared, but still with 2 of the 3 attachments gone. I've only experienced this on my Chromebook.
This is a serious problem with Evernote randomly removing attachments with no means of recovery.