One spouse cannot file Married, filing jointly and the other spouse files Married, filing separately. Since you two filed separately initially, yes, you can change the filing status to Married, Filing Jointly, but in the 1040X amended tax return, the return must include income, deductions, tax payments, etc. of BOTH spouses.
When you filed the amended tax return, did you include both spouses income, deductions, tax payments and previous refunds?
As a general rule, the IRS has three years to challenge your tax return under the Statute of Limitation. NO, past refunds are NOT "settled transactions" unless the statute has passed. The statute for 2023 generally doesn't pass until April 15, 2027.
TurboTax generally does a good job calculating the tax return. But the input has to be correct.
