I can't totally remember this as it's been a few clients ago that I've had to deal with COA profiles. But I think if you see look at the table KOTI002 you'll find your records. I THINK that deleting the record in SAP only causes an update to the "Valid To" field in the table. The actual record remains.
Especially once a cert or assignment is used, the system doesn't want it deleted. You may decide to go back and reprocess and old output at some point.
Craig