You can amend a Married Filing Joint (MFJ) return to a Married Filing Separate (MFS) return and vice versa. When amending a MFJ return to a MFS return, first delete all information associated with the spouse on that return. This includes all Form W-2s, Schedule Cs, Schedule SEs, etc. Anything that can be denoted as '"Spouse" needs to be deleted. Once those items have been deleted, change the filing status to MFS.
Note: Changing the filing status from MFJ to MFS has to be done before the filing deadline. After the filing deadline, you CANNOT amend your filing status from MFJ to MFS.
When changing from MFS to MFJ, select the taxpayer you'd like to be the primary taxpayer. Change the filing status to MFJ, then add all information pertaining to the other spouse.
Note: Once the tax return has been filed as Married Filing Separate (MFS), you have three years from the original deadline to make the change to the tax return. This deadline DOES NOT include any filing extensions.