Thank you for the details, Alex.

Normally when matching transactions, the VAT used on the transaction in QuickBooks will be retained. The VAT on the bank transactions will not affect or replace them. 

Let's do the basic troubleshooting steps to see if this is caused by a browser issue.

To start, you'll want to sign in to QuickBooks using a private browser. This step disables its extensions and stops the cache from saving your browsing history.

• Google Chrome: Ctrl + Shift + N
• MS Edge and Firefox: Ctrl + Shift + P
• Safari: Command + Shift + N

If your invoices will retain the VAT, you can go back to your regular browser and clear its cache. If not, please try other browsers to see if we get the same thing.

If nothing works, please contact our Support team to check this further. They can start a screen-sharing session to gather more details about this behavior.

Feel free to share an update after doing the steps above.