Undeposited Funds

No, a Journal won't fix it. The only way to get rid of them is either to delete the payments (if they didn't happen, for example) or deposit them, if they did. 

If the reason they're there is because, while they were in reality deposited, but the deposits weren't created correctly to include the payments, then edit the deposits, click the Payments button at the top, and add the appropriate payments to the deposit. Then delete whatever detail was initially on the deposit and then, when the deposit total amount is the same as before you edited it, save it.