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To Mark Transactions as already processed, you first need to run a special function to turn on this option. Go to File → Utilities.
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Scroll until you see the Toggle Mark Already Processed Button and click to select. Then, click Run Special Function.
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Click Ok on the pop-up letting you know you can now mark records as already processed, and then click Close.
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Next, go to Program → Ledger → Deposit Processing.
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Select the deposit that has already been entered into Ledger and then click Mark Already Processed.
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Click Yes on the pop-up asking if you are sure you want ot mark the selected deposit as already entered.
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You will then no longer see that transaction under Deposits.