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Yes, based on the information you provided, you will need to amend. Not because you need to withdraw the money, but because you reported that you overfunded it. If the tax return computed that you overfunded, but you have verified that you did not, you need to correct the error.
According to Why am I showing an excess HSA contribution?, the 2024 maximum for both employer and employee HSA contributions was as follows:
Compare the limits above (plus $1,000 if you are 55+) to what you reported on your tax return. You can find this by looking at your completed tax return, form 8889, line 11. Form 8889 Line 11 should be the sum of what you and your employer contributed (Box 12, Code W from your W-2) plus any contributions you made directly to the HSA, not through payroll. If there is a difference in what you reported versus what you contributed, you should amend.
Here is some more information on filing amendments: How to File an Amended Tax Return with the IRS
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