Once the IRS has processed your Tax Return and you have received your Refund, you will need to Amend your Tax Return to include Form 8889.
You will report your HSA distributions on Form 8889 and deem which portion of the distributions were for Qualified Medical Expenses. If 100% of the distributions were for Qualified Medical Expenses this will have no effect on your refund.
If you do not Amend and file Form 8889, the IRS will deem all of the HSA Distributions as non-qualified and will add them to your Taxable Income. Basically, filing Form 8889 lets them know the HSA Distributions were a non-taxable event.
See TurboTax FAQ below on how to amend your return:
https://ttlc.intuit.com/replies/3288565
