Each form reports something different ... the 5498 shows the contribution and the current value of the account (and is mostly informational only and there is no place to enter this form at all ) where as the 1099 shows the distribution taken during the year.
The HSA is handled in 3 parts in the TT program :
https://ttlc.intuit.com/community/health-care/help/what-is-a-health-savings-account-hsa/00/25765
First the contribution:
https://ttlc.intuit.com/community/entering-importing/help/where-do-i-enter-my-hsa-contribution/00/26...
https://turbotax.intuit.com/tax-tips/health-care/what-is-the-irs-form-8889/L8hRNHx4o
Next the limitations screen to confirm you are eligible to make the contributions:
Until you complete the HSA portion of the TurboTax interview to establish your eligibility for an HSA contribution, TurboTax will treat the amount entered on the W-2 form as an excess HSA contribution.
https://ttlc.intuit.com/community/health-care/help/why-am-i-showing-an-excess-hsa-contribution/00/26...
And lastly any distribution:
https://ttlc.intuit.com/community/health-care/help/why-is-my-hsa-distribution-taxable/00/26609
