What would be the consideration of deduction if a part of 1 BoQ Item has to be cancelled where unit cost breakdown was not submitted nor recorded?

It's important to ensure that such deduction will be requested and executed in the 'Contract Clause' and mutually agreed between the contractor and client. It's also important to specify the process that will be followed to address such instances. Typically, once such cases are spelt in black and white in the contract document, the best process would be to get the RFI (request for information), ask for cost reductions, document the change through change management process and get this aligned and approved prior to execution of that item.