If anyone is still struggling with this issue, here's the steps to re-verify your domain:
Login to your developer account and click "Certificates, Identifiers & Profiles"
Click "Identifiers" from the sidebar
At the top right of the screen, next to the search icon, it'll probably say "App IDs," click it to reveal the dropdown menu.
Select "Merchant IDs" from the dropdown menu and the list should update with your payment identifiers
Click on the identifier you need to re-verify
You'll see your "Merchant Domains" listed under "Apply Pay Payment Processing on the Web." Click the "Verify" button.
You'll need to download and then upload the new "apple-developer-merchantid-domain-association.txt" to the ".well-known/" directory on your server.
One you do, click "Continue" and your domain should be re-verified.
Hope this helps!