You'll file two superseding returns (one for each spouse). They'll need to be paper filed, I would write "Superseding return" at the top and make sure everyone "ink" signs before mailing certified.  If the MFJ return showed a refund then you'll need to attach a statement to the returns indicating how you have decided to split the refund between the two tax returns (be consistent!) and indicate how much additional refund you are expecting for each MFS taxpayer.

My expectation will be that it will take the IRS 8-10 months to sort this out. But at least they'll pay interest (and at a rate better than any bank in town!)

Rick