I managed to fix it - 3 notes I created in 2016 seemed to not have synced properly, after deleting them I can export all notes in one batch.
These were the steps I used find and delete the notes with missing content.enml files:
You have to repeat the process each time the error message shows when exporting if you have multiple notes that cause issues.
I think its really poor from Evernote to have bugs in the export process for so long, and also to not offer exporting notebook names - I have 100s of notebooks, it would take me all day to manually export them. Also their security bug bounty is 10-100x less then their competitors - do not trust Evernote with private notes.