This was a strange occurrence on our production Server so I decided to capture the incident just-in-case.
5:58AM -- I logged on to our Server, 10.0.1, and went to the Project of the workbook to delete. I clicked the ellipsis for the workbook, selected Delete..., and clicked the red Deletebutton. The screen refreshed but the workbook was still present. Odd. So I clicked the ellipsis again, selected Delete..., and clicked the red Delete button again. The screen refreshed, the workbook was gone, but I got the pink error message at the top of the screen. I clicked on the Details link and got the below:
So it would seem that the workbook did get deleted the first time but somehow the screen refreshed faster than the internal db was able to process.