It's good that you're able to update the VAT number in the settings, craffordshaun7.
In QuickBooks Online, we can only add the Business (CIPC) Reg. No. It seems that you're using a custom field to include the VAT number. If so, we can just manually change it when creating an invoice.
In addition, you can follow these steps if you entered the VAT number in the Business (CIPC) Reg. No. field:
Go to the Gear icon and select Custom Form Styles.
Locate the invoice template and click Edit.
Select the Content tab and click on the header section of the invoice.
In the Business (CIPC) Reg. No. field, update the number.