Invoicing based on percentage of completion with 10% retention deducted on the invoice which is payable after the warranty period?

Retention/Holdback accounting - There is more than one way to accomplish this.

Create a Retention receivable account (current asset), and a Retention item which links to that gl account.

Then add the retention item to the bottom of your invoice as a (negative) amount. - This can be done when you first create the invoice - or be added after the customer pays 90%.

At the end of the warranty period issue an invoice using only this item for the amount due.

Check on you local rules for the sales tax rules on the holdback - it may or may no be a taxable item.