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If you filed separately on original tax return than you can amend and change a return to married filing jointly. You can't, however, do the reverse. Changing from joint to separate filing after a return's deadline is past is not allowed. You will only file one Form 1040X.
Here is an extract from Form 1040X instructions for your reference-
Enter in column A the amounts from your return as originally filed or as previously adjusted (either by you or the IRS).
Combine the amounts from your spouse's return as originally filed or as previously adjusted with any other changes you or your spouse are making to determine the amounts to enter in column B. If your spouse did not file an original return, include your spouse's income, deductions, credits, other taxes, etc., to determine the amounts to enter in column B.
Read the instructions for column C on this page to figure the amounts to enter in that column.
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Please note: This advice is provided with the understanding that all the relevant facts have been provided by you. Any change in facts might affect the advice given and hence may not be relied on in such cases. Nothing contained in this reply was intended or written to be used, can be used by any taxpayer, or may be relied upon or used by any taxpayer for the purposes of avoiding penalties that may be imposed on the taxpayer under the Internal Revenue Code of 1986, as amended.
Yes, you file only one Form 1040X.
Report the amount you reported on original return in Column A.If you are using a tax software than input your spouse income and other detail in the software. The software will automatically calculate the amounts to be entered in Column B. If any adjustments were made by the IRS after tax return for your spouse was filed or if she received any refund or paid any tax than you might want to adjust that on the tax return Column B too.
Column C would include the income for both of you and the deductions allowed based on married filing joint returns.
You will prepare a return as married filing joint including the income of your Spouse. This will be the correct income tax return. You will than include in Column B the amounts so that column c matches the correct income tax return. Any adjustments for taxes on your spouse tax return will be included on this return.
You do not have to amend your spouse return to show she is not filing as single. IRS will get that info from your amended tax return.
I would suggest you to use a tax software to assist you with preparing an amended tax return.