List each donor separately when recording the deposit in Banking -> Make Deposits. For the pledge payment, select the donor's name and link it to the correct pledge receivable account or income category used for pledges. For the other donations, categorize them accordingly (specific fund accounts).

If the pledge payment was recorded earlier as an open receivable, apply the payment from the deposit screen instead of creating a new deposit. Otherwise, QBO might assume the deposit is new income rather than fulfilling an existing pledge.

If QuickBooks is still creating a duplicate, check if the original pledge was recorded as an invoice or sales receipt. Adjustments might be needed to ensure it's properly matched.