Nothing you can put on a Form 5329 will inform the IRS that you obtained a timely return of excess contribution.
Filing Form 5329 just to show zeros on lines 47, 48 and 49 cannot be done by e-filing. You would have to mail your tax return which could delay processing by 6 months. Because you obtained a timely return of excess contribution, line 47 MUST have a zero on it.
The IRS will be aware of the return of excess contribution by the code-2 2023 Form 1099-SA that the HSA custodian will issue. The IRS is well aware that the corrective distribution more often that not occurs after the end of the tax year (but before the due date of the tax return).
