There is also a nice QlikView tool that will help you with the detection of CAL anomalies. Useful if you often experience things like this. Also useful if you want to know how many Doc CALs are assigned to users (without checking individual document assignments, can become tiresome), and how many of them should get a Named CAL instead.
Create 2 qvw files with the same name and in the same location of the docs you deleted. These 2 new files can be empty, the only thing that matters is that the name is the same name as the files you deleted. Then you can go to the QMC and remove the doc CALs.