There are a few of errors in this process. The Instruction should have been given prior to the quotation being submitted, if they wanted to know the cost up front this should have done through a Proposed Instruction.
With regard to when the action is taken, once the instruction is issued, the scope should be inserted in to the Contract programme when it is practicable to complete and then the outcome on the Planned Completion used to quote the time based element of the quote. It cannot be done before it can be done.
Second point is each individual instruction requires it’s own PMI and it’s own CE. They cannot group them together especially if they relate to different issues. They should be instructed separately and quoted separately in chronological order to allow the time and cost to be transparent. The PM can only do an assessment if you did not provide a quotation within the time allowed or the quote you did submit was not in accordance with the Contract.