I think you mean you have a Healthcare Reimbursement Arrangement (HRA) with your employer. That does make you not eligible to make HSA contributions.
For 2023 you need to file an amended tax return to report the ineligible contributions. It will have a form 5329, and a form 8889 (but there should already be an 8889). You will pay income tax on the contributions (because you lose the deduction) plus a 6% penalty.
For 2024 you need to file an amended tax return to report the ineligible contributions. It will have a form 5329, and a form 8889 (but there should already be an 8889). You will pay income tax on the 2024 contributions (because you lose the deduction) plus a 6% penalty on the combined balance from 2023 and 2024.
Note that the penalties are 6% of the ineligible contribution, or 6% of the account balance as of December 31 of the tax year, whichever is less. So if you spent some of the money, your penalty will be less than 6% of the entire contribution.
If you used tax software to file your 2023 and 2024 returns, you can use the same software to amend. Just change your answer on HSA eligibility, and the program should figure out the consequences. If you filed by hand, and are comfortable doing that, you can probably file the amended returns. An amended return would be a copy of the new return with the new (corrected) information, plus a 1040-x to summarize the changes.
For 2025 you have already removed the excess 2025 contributions so you only need to deal with the accumulated excess from 2023 and 2024. If you withdraw the funds, you will pay income tax plus a 20% penalty (rough estimate 44% tax). If you don't withdraw the funds, you will pay 6% a year for every year the excess funds remain in the account. But that 6% is based on the account balance, so if you draw down the funds for medical expenses, the penalty will be less every year until you use up the funds. So if you think you can use up the funds for qualified medical expenses in 5 years or less (roughly speaking) then you will probably pay less tax in the long run by leaving the money in the account and paying 6% per year until you draw it down to zero.
There is another option if you think you will be eligible to make new contributions in the future, but I think you said that's not on the table so I will not discuss that option for now.
If you want to withdraw the funds now, pay the massive tax, and get it over with, just make a regular withdrawal, and don't use it for medical expenses (and tell your tax software that is was not used for medical expenses). You can't make a special withdrawal of those older deposits, it has to be a regular withdrawal.
