how do I issue a partial refund

Cannot do it on the invoice. 

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You are paid to paypal, so that is where you make a refund. You click on the payment, and use the refund link, just amend as required!

 

If you mean you have not yet been paid, then you amend the postage on the invoice > More Actions > Send Payment Details.

 

You cannot amend the sale price.

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