If you will change from MFS to a joint return with a spouse who has already filed then the spouse's filed return must be AMENDED not superceded. It cannot be efiled due to the change in filing status and since you will have an additional refund you have 3 years to amend the original return. Amending the spouse return to add you WILL report a return filed in your name ... why ever would you think it would not ? Just be aware that amended returns are taking 6 months to a year to process so patience will be needed.
Of course you could just file your own return now and amend one of them later to marry up the 2 returns ... again you have 3 years to do so ... don't be in a rush... it will take time for this loan forgiveness to happen.
