This HSA custodian (or at least the representative you are dealing with) is clearly incompetent. They need to read and understand the instructions for Form 1099-SA and 5498-SA. They also need to read and understand IRS Notices 2004-50 and 2008-59 where these discuss excess HSA contributions.
The instructions for box 2 of Form 1099-SA indicate that this box is only for reporting the amount of earnings on a contribution returned before the due date of the tax return. That's impossible for the $475.01 contribution made for 2021 because that deadline has passed more than 9 months ago. As I've stated previously, the Form 1099-SA reporting the distribution of the $475.01 must have $475.01 in box 1, nothing in box 2 and code 1 in box 3. You should just request a regular distribution to you of $475.01 and say nothing about it having anything to do with an excess contribution. You treat it as resolving the excess contribution for 2021 by how you will report it on your 2023 Forms 8889 and 5329 as a regular taxable distribution.
They should not be changing any Forms 5498-SA. Doing so would create a disagreement between amounts reported on the Forms 5498 and the amounts shown with code W in box 12 of your Forms W-2. The only reason that a Form 5498-SA would be changed with regard to an excess contribution is if the HSA contributions deposited by your employer exceeded the annual statutory limit and the employer requested that the excess be returned to them (along with a corresponding change to your W-2), neither of which happened in this case.
I have no changes to what I have stated needs to be on the Forms 1099-SA.
