No. Acceptance of the counter-offer is a valid changed circumstance. It doesn't start a new transaction. It continues the one begun with the original application. Dan's reply from the thread I linked says:
You will deny the loan as applied for with the counteroffer. If the applicant indicates they want to proceed with the counteroffer then that would be a applicant requested change allowing a new GFE to be issued at that time.
That doesn't mean you give a denial. It means the counter-offer is denying the original request and suggesting another.