Yes. You will need to Amend Your Return to enter the 1099-SA and the 5498SA. Prior to clicking the amend button, be sure that your return is original (meaning, if you did not enter any additional information after you filed)
Then you can go through and amend your return once the refund amount or tax due is set back to $0.
On the amended return, if you see a tax due, this would include a repayment of a refund (if you received one) that was more than you should have received if your return would have been complete when it was submitted.