It won't go through if you're using more than two currency in a single transaction. To receive the payment from the EUR currency, you’ll have to create a clearing account that has the Home Currency ZAR.
First, create a bank deposit from your EUR Bank account.
Click the +New icon.
Select Bank Deposit and choose the account EUR bank.
Received from GBP customer and hit Save and close.
Here’s how to add a clearing account.
Go to the Accounting menu.
Select the Chart of Accounts and click the New button.
Complete the Account details and choose ZAR as the currency of the account.
Hit Save and Close.
Then go to the GBP Invoice and receive the payment using the clearing account. This will zero the balance to your clearing account.