When you actually physically make the bank deposit, you need to go into Banking > Make Deposits, check off the undeposited funds that are included on the deposit and then finish the deposit.

If you’ve deposited the funds already, without checking off the undeposited funds, you can create a $0 deposit that includes the payments shown on the undeposited funds screen that have already been deposited. You’ll need to find the deposit you already entered and check to see what account was used on it. Then make a new deposit checking off the undeposited funds, and add an additional line using the account from the other deposit you already entered with a negative amount bringing the deposit down to $0.  If you have to do many of these, you might want to create a special bank account called “clearing account” so you don’t clog your real checking account up with $0 transactions.

You can also use Client Data Review to fix undeposited funds.  It’s a feature in the Accountants edition of QuickBooks Premier and Enterprise.  You can also turn on limited features in other versions by creating and logging in as an External Accountant user.