I experienced the same issue. I was prompted to upgrade, which I accepted. I downloaded the installer and followed the prompts. At one point, Evernote recommended to accept removal of the old version, which I did. When I opened the upgraded version, all of my notes and notebooks were GONE!!
I am beyond upset that the installer is not programmed to retain all the previous information. And because I have the free version, I am relegated to posting in a discussion forum about this as I am now with no real person help!
Bottom line: Do NOT upgrade, and if you do, do not allow the installer to remove your previous version!
I will also add that the sync option is missing from the new version!