If a payment was made on a Sale Order and then removed, you should be able to see this payment as a customer credi tin Cin7-> Sale -> Customers/Credits -> Search for the Customer.
If the credit isn't showing there as a Customer Credit, you can use the resync payment from Pencil -> Sales Orders by follow the steps here:
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Go to Sales Orders -> Search for your Sale Order Number.
2. Click on the (...) More Actions -> Click on Payment Details -> Then click on the Sync Button.
Popup will look like this. Click Sync Button.
3. Wait 30 seconds and go back to see if the payment has been applied to the Sales Order number or is showing as a Customer Credit