I have been experiencing this issue for some time and I have noticed that all my affected notes contain at lease one checkbox. I realized it since I am also a TaskClone user and I use the checkbox a lot for that. I started to see notes that had been updated and I knew I had not looked at them for months. When it happens, I usually see a batch of 5-8 notes that have the same update timestamp and all have simply been moved to the default notebook. Unfortunately, this has made me stop using both checkbox and TaskClone. I chatted with Evernote support 3 days ago and was told I might be contacted by someone in the technical area. So far, I have not heard from anyone.
If this is an issue that will take some time to resolve, Evernote should at least do a notification to users.