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You cannot amend a tax return that was filed Married Filing Jointly to Married Filing Separately after the due date of the tax return.
When did he amend? You can’t amend a joint return to MFS after April 15. See note at top of this article
See Expert Susan's post about the rules for amending Joint to Separate returns
Just because it was accepted by the e-file system (passed basic validation checks) does not meant the IRS has agreed or will allow it.
Amending from joint to separate is not allowed after the original due date. The only time it might be permitted is if one of the spouses is going to allege that they never agreed to file jointly, and the other spouse used their name and SSN and e-file pin without permission (i.e. committed fraud). You should not go down this road without appropriate legal advice.
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