@SilverCloud Create an "Account Credit" DISCOUNT with a $0.00 dollar amount. Create your invoice adding the pre-paid discount minus Taxes. You will have to charge a non taxable fee "Uncollected Tax" that equals the tax on $50 charge. This workaround is assuming you all ready closed an invoice/transaction as a non-taxed deposit. If not you can charge full amount and refund the $50 deposit.
Note: This will be added to your overall numbers as a discounted revenue.
It would be nice if we had a "Partial Payment" override with corresponding invoices/receipt. Kind of like "Refunding" works when it ties the refund to the invoice/receipt. Square could always give us the ability to add a negative modifier. Just saying...
