I think you need to find a local professional to sort everything out for you, especially since you amended her Married Filing Separate return. You will need to stay with that return and amend that amended return to make it a Married Filing Joint return.
I would file an extension for now and make an appointment with a local professional. We can't help you in this environment without seeing what you originally filed and the originally amendment. You do not want to file another return.
It depends on what program you are using. See your options here: How do I file an IRS tax extension? - TurboTax Support - Intuit
This will extend the time you have to file your taxes until October 15th, 2025.
Also, you may have to do your state taxes: Do I need to file an extension for my personal state taxes?
Remember, an extension gives you more time to prepare your taxes, but it doesn't extend the time to pay your taxes. If you have an indication that you will owe taxes, you should make the payment by the original due date of the tax return to avoid additional interest and penalties.
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