Fee % on Pricelist Items NEC Short Contract

I am currently working on an NEC Short Contract with a pricelist, some elements of the work have been omitted, and additional work instructed.

If i am able to price this using rates from the pricelist am i still entitled to the fee %? Similarly, should the Fee % be added to the works omitted?

Thanks

The rates in the price list should already have the fee incorporated within them.