For everyone having this issue. I had a session with Josepth from the support team today and figured out a solution.

Basically you need to disconnect Wise entirely and connect again, but you need to log out from Quickbooks for the change to reflect after you disconnect.

I am not sure all of the steps are necessary, but this is everything that what we did:

0. Find which account in the chart of accounts corresponds to the Wise bank account, remember the name and the date of the last transaction pulled from Wise.
1. Log In to Wise
2. Go to Settings -> Connected Accounts
3. Click on "Manage" under Quickbooks.
4. Click on "Advanced Settings" & enable "Sync bill and invoice payments", click on Save. It might prompt a reconnection and consent window. You can disable it again later.
5. Go back to Quickbooks.
6. Under "Manage Connections" disconnect Wise.
7. Log Out and Log In again.
8. Go Back to "Manage Connections". If you can't find it now it's under the dropdown menu next to the "Link account" button in the "Banking" screen.
9. Connect Wise again, use the information from step 0 to map to the chart of accounts and the date of the transaction last synchronized.

It's not ideal and there is definitely a dead button in the QB interface, but this might get you unstuck for now. 

Hope it helps.