I appreciate you for posting your concern here in the Community, @andrismcgee.

QuickBooks Online (QBO) will automatically calculate the FLAT Rate Scheme (FRS) depends on how you set up the VAT code and settings. 

You can review your VAT settings to make sure that all of your transactions in QBO uses the 20% VAT rate.

Here's how: 

1. In the left tab menu, select Taxes.
2. Click the drop-down arrow next to Edit VAT and then choose Edit Settings or Edit Rates.

For additional reference, you can check this article to learn more on how to set up and edit VAT settings, VAT codes and VAT rates. 

Since the FRS has already been submitted, I recommend consulting with HMRC on how you can correct the incorrect submission. If you're advised to re-submit it, I encourage you to contact our QuickBooks Online Support Team to further assist you with the steps.  

Here's how to contact our customer support:

1. Sign in to your QuickBooks Online company.
2. Select Help (?) at the top right.
3. Click Contact Us to connect with a live support agent.

For additional reference, you can check this article to know more about Flat Rate Scheme.

I'll be around to help if you have any other questions. Wishing you and your business continued success.