You will have to re-apply it on your next years tax return, but you can keep forwarding any refund amount to estimated taxes.  TurboTax will give you this option to apply any refund to estimated taxes during the interview.

Example:  You have a $6,000 refund in 2016 and are scheduled to make estimated tax payments of $3,000 for 2017.  You can apply the whole $6,000 refund to your estimated taxes for 2017.  Then, when you file your 2017 tax return, you can apply any refund to your 2018 estimated taxes.  Lets keep it simple and say everything stays the same so you have a $3,000 refund in 2017.  Now, you can apply it to your 2018 ES taxes.  But, you will have to mark that option on your 2017 return.