NEC3 ECC: Omitted some areas of work to save time and money

The client has omitted some areas of work to save time and money. The main Contractor has confirmed the saving on the omissions but is claiming loss of profit on the omitted items. The reasons for the omissions is to pay for other compensation events that have occurred. Does the contract allow for this?

No. The omitted works is a compensation event, which should include the defined cost estimate as to what the works would have cost PLUS the fee, so they do not get to retain it.