I was trying to import a lot of notes from Evernote and kept running into problems on certain notes. I figured out that this was Evernote’s exporting problem – it couldn’t even re-import its own notes in some cases.
What fixed it was realizing that I could use Evernote Legacy (mac version link) on the problem notes. The exports work successfully there. I suspect some formatting in some notes might not export as completely as with the Evernote main version, but that’s why I only use it on the problem notes.
For example, in my case I had 6000 notes. The first 5000 or so exported just fine with regular Evernote. I used Legacy on the last 1000.