Assuming there are no Z clause amendments then the completely wrong process has been followed here.
Acceleration is a stand alone process, that does not go through the CE quotation/assessment/implementation process. If the Contractor instructs a quotation for acceleration then the Subcontractor submits a quotation and the Contractor either accepts or "rejects" the quotation. If they reject, nothing happens - Completion Date doesn't move and nor does the total of the Prices. If the quotation IS accepted, then Completion Date moves forward , they are paid the money but their liability to Delay Damages are now at the earlier date. The quote needs to be agreed before the Subcontractor puts into place the acceleration measures (and if they have that would be at their risk).
As you describe the wrong process has been followed so you need to channel it all back into the correct process I suggest. I don't think the deemed acceptances are relevant here as they should not have followed that route.
Acceleration is a stand alone process, that does not go through the CE quotation/assessment/implementation process. If the Contractor instructs a quotation for acceleration then the Subcontractor submits a quotation and the Contractor either accepts or "rejects" the quotation. If they reject, nothing happens - Completion Date doesn't move and nor does the total of the Prices. If the quotation IS accepted, then Completion Date moves forward , they are paid the money but their liability to Delay Damages are now at the earlier date. The quote needs to be agreed before the Subcontractor puts into place the acceleration measures (and if they have that would be at their risk).
As you describe the wrong process has been followed so you need to channel it all back into the correct process I suggest. I don't think the deemed acceptances are relevant here as they should not have followed that route.