What do I do if I have issued an invoice but customer comes back and pays cash?

Hello Flex1, 

You need to make sure you have a petty cash account in the chart of account first before you can do this. 

once you have a petty cash account this is what you need to do to show this in your account 

Go to the invoice>click on receive payment top right> the receive payment page will open>make sure only the invoice you need is ticked>payment method would be cash>deposit to would be the petty cash account>save and close bottom right.