NEC3 ECC: How can credit value of Equipment can be deducted from PWDD if SCC23 is not used?

It sounds like you have an amended Schedule of Cost Components if 23 has been deleted. That and any such amendments have to be taken on face value. The Contractor can claim the elements included within the SCC and nothing else. If there is a cost that is not covered then it is deemed to be included in the fee.