"Will this be an issue since the 1099 and 5498 don't reconcile to my tax return?"
I assume that you are referring to the 2023 forms. This is not an issue because it will reconcile in your tax account once the HSA custodian issues the 2024 Form 1099-SA early next year. The IRS is well aware that returns of excess HSA contributions commonly do not happen until the year after the year for which the excess contribution was made.
The earnings will be shown on the 2024 Form 1099-SA which will be taxable on your 2024 tax return as required by the tax code. (You should already know the amount of attributable earnings as the difference between $1,463 and the amount that was distributed.)
