A similar thing happened to me all through evernote web. I accidentally deleted a notebook and all the notes in the notebook are gone. They are not in Trash.
This is a huge flaw. specially for a premium account. Is there any way I can recover my notes?
Update: this is the workaround that I discovered. I switched to older version of evernote GUI and there they were! in the trash! This must a be a bug because reload the new GUI web did not show me the lost notes. I would have also liked the notebook itself to be in the trash