Why do you think you have an over-contribution?
An HSA is an individual account. You can have one, your spouse can have a separate account, but there are no joint HSAs. Your ability to contribute to your account is determined by what kind of insurance coverage you have, and is not affected by your wife's coverage. If you are covered by a qualifying HDHP, and have no other disqualifying coverage, then you can contribute to your account, even if your wife stops being eligible to contribute to her account. And it doesn't matter if the "owner" of the insurance policy is you or your spouse, it just matters how you are covered.
And that would make your attempt to remove an excess contribution incorrect, and somewhat difficult to deal with. But I think it can be put back.
First, let's confirm you and your wife's eligibility. What kind of insurance did you have for 2025?