Function Module "CRM_MKTBP_DEL_ATTR_BP_LIST" will delete marketing attribute set also when there is not even single attribute belongs to it is not assigned with any value. In your case, you had two value assigned and you deleted them using this FM. So at end FM delete attribute set also from BP.
If you want to have attribute set to be still assigned with all/any marketing attribute having now value selected than there must be at least one marketing attribute out of all attributes with some default value. Try this in SAP GUI screen, adding marketing attribute set with no attribute with any single value and save, you will get error message"Select at least one attribute with one value".
Regards