The calculation is done at the point of the vat return being generated.
If you are doing quarterly periods, 1 rate would be applied, If however you are doing monthly returns then you could adjust it before each return is generated.
I’m doing quarterly periods as things stand and so my Flat Rate percentage changes during the period.
Is there a way to accommodate this in Quick FIle?
At this point, I’m wondering if I should just overpay my VAT for this quarter, ignoring the 1% discount and paying at 12.5% for the three months, then claim it back next month.
I would suggest you make a manual adjustment to the VAT return to account for the difference in the two rates. I would set the flat rate to the new rate, and then adjust for the discounted amount in November to December as a manual adjustment in Box 1.