Hi Valy,
Absolutely! If you've already used the 'Receive Money' transaction to apply refunds from the double payments, you might find yourself with debit notes that can't be applied because the double payments have been taken care of. Here's a simpler way to deal with this: You should remove the deposit transactions (receive money) and apply them again using the 'Receive Refund' in the Purchase Register. But it might be a good idea to get in touch with your accountant while doing this. They can give you advice that's more suited to your situation and help you make sure everything is done right.
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Kind regards,
Shella