I changed our status from married joint to separate. Will the software handle the change?Or do I need to delete one person and file another return for the 2nd person?

Just prior to filing married, filing jointly, I changed the status to married, filing separately.  Does the software handle this?  Can we file one return with this status or do we now have to file two separate returns?

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If you make the adjustment in the software, you should be able to just walk back through the questions and answer them for each individual and the software will prompt you to do a return for each person and you can file them both at once.