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After you file
Only ONE MFJ return was filed so that is the ONLY one that needs to be amended. By removing the spouse's info on the 1040X the spouse is now considered to have not filed ... they will have to mail in an original return with a copy of the original and amended returns attached.
BUT BEFORE YOU AMEND ... be aware that if one of you uses the itemized deduction then both of you must itemize OR both of you will use the standard deduction. And some deductions and credits are not allowed. So before either of you put a return in the mail (efiling will not be allowed) make very sure you want to amend.
Also be aware that amending will most likely NOT get you a third stimulus check this year ... it did not happen last year for those who amended after filing the first time so you may be wasting your time for nothing.
The third stimulus check will be reconciled on the 2021 return you will file next year and you may look to see if filing separately will be better. It may cost you more in federal taxes than the stimulus money you will get.