Incorrect Tax Calculation and Self assessment done after that

Hi, For the tax year 2023-2024, I had received an email from HMRC that I have underpaid tax and that I need to pay the tax owed balance by 31-Jan-2025. After this message, I had done a self-assessment tax return for 2023-2024 and ensured my SIPP contributions and amounts from my employer where reflected correctly. This shows that I have overpaid and hence initiated a refund of the tax overpaid. Now, what happens to the original tax calculation by HMRC? as I haven't received any further update from HMRC? Thanks 

Hi,
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