This is still an ongoing issue. My only solution is to delete evernote from your device, then reinstall it. Don't change the default notebook when clipping. Afterwards, just go into the evernote app and change notebooks there. If you select a different notebook while clipping, you will break it and end up exactly where you are now.
Note: If you have to clip a pdf from the web, email it to your evernote account. Don't use everbroke clipper. It can't do pdf's without breaking.
This is the only solution. The evernote tech support is non-existent, or worse, doesn't appear to care about its customers (...and I'm a Premium Evernote Business Customer for many years now).
If you find a better solution, please let me know. It will brighten my day.