H Jordan, was your issue resolved? I have exactly the same problem. I have a note that was created several months ago and I am 100 % sure there was a zip file attached. I didn't open the note for a long time and now the attachment is missing.
I don't have premium, so I cannot check the history 😕
Have to say that I am very disappointed. What is the point of using Evernote if it's that unreliable?