How do I clear an amount in undeposited funds that was caused by a credit memo?

I appreciate the detailed information, TEV33. Let me help you resolve your issue.

I've replicated your concern. Once you apply the credit memo to an invoice, you'll have to select the credits, and the amount will be added automatically in the payment field. If the credit is lesser than the invoice amount, you'll have to enter the remaining value in the payment field. If they're of the same value, you don't have to re-enter the payment amount. 
 

However, the credit memo amount will not show on the Bank Deposit page since it will not affect the bank balance. It will only affect the customer's balance. You can refer to the screenshots below:

You'll have to deposit the payments in the bank account to clear the Undeposited Funds.

I'll add this article to help you learn more about credit memos: Create and apply credit memos or delayed credits in QuickBooks Online.

If you have additional questions regarding your concern, you can always get back to this thread. Take care!