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First step is to Unapply the invoice and payment from each other.

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Select Unapply Entries
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Then Unapply – and say yes to unapply
The entries are both open again
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Go to the General Journal
Enter in the Date, a Document No., Account Type is Vendor, select your Vendor No. then go to Apply Entries

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Select the payment line, then Actions, Set Applies-to ID

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When you select Set Applies-to ID – it will drop in the Document No. and then you select OK
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This drops in the amount on the line –
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Then you just need to add the balancing account of what was used in the Payment Method
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Then you are ready to post