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Create a Credit Memo
Go to Sales.
Click Sales Credit Memos.

Select New.
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Select the Customer No.
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You can enter in the External Document No. the invoice number this is to clear.
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Enter in the Sales Line from the Sales Invoice you are creating the Sales Credit memo for in this example it is for an Item.
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Then. Post.
Then.  Apply the credit memo to the invoice.
Go to the Customer card, Related, History, Ledger Entries.
Select the Credit Memo.
Click Process, Apply Entries.

Select the Invoice to apply, Click Process, Set Applies-to Id.  This will put your user id in the Applies-to ID column.

Click Process.  Post Application.
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Click Ok.
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Now.  When you review the Customer Ledger Entries the remaining amounts for those two entries will be zero.