If we send a TEXAS Notice of Contractual Retainage for 5%, as that is what the agreed upon retainage is, will it affect the other amounts that are due from previous payments that were short paid?

We have a contract in place with a Contractor and our role is Material Supplier. The payment terms offered to them were 95% upon manufacture completion (ready to ship) and 5% upon start-up. They have only paid 90% and we have been having a hard time getting the other 5% from the first payment. Now we are at a point where start-up has been completed and is due (however, they have Net 60 days from start-up to pay that 5% - making it due on 10/28/18). We just prepared an order for the Notice of Contractual Retainage to be sent out and listed the retainage as 5% and the amount as $13,629.00. Total balance due to us is 10% and the amount is $27,258.00. By doing this, are we hurting our rights to the other 5% that is past due?