Amend your return. You actually won't need your 5498-SA, but you need to enter your 1099-SA or else your form 8889 won't be completed correctly. The IRS matches the entries on the 8889 against the 1099-SA that the received from your employer.
If the IRS accepts your return, you will need to amend your return in order to make any changes. Note that form 1040X is not quite ready yet at TurboTax; it is expected to be available in early February – see https://ttlc.intuit.com/questions/1908854-irs-forms-availability-table-for-turbotax-individual-personal-tax-products
In any case, you want to wait until your original return has been processed by the IRS, so that it and the amended return don't collide. The usual suggestion is to wait until you get notice of your refund, because this means that the IRS has finished its processing
How to check e-file status - https://ttlc.intuit.com/replies/3319882
To check the status of your federal tax refund, go to Where's My Refund? at IRS.gov.
For information on how to amend your return, please see https://ttlc.intuit.com/replies/3288565
If, however, your return is for some reason rejected, then you don't have to amend your tax return. Just return to TurboTax and make the corrections you want, and re-file the return.
How to fix a rejected return - https://ttlc.intuit.com/replies/3302275