@pk
I don't see how they passed the substantial presence test by the end of 2023. They only entered the U.S., for the first time ever, on July 8, 2023. July 8 through December 31 is only 177 days. The substantial presence test requires 183 days. So I don't think they met the substantial presence test until January 6, 2024.
If I understand correctly, that means that they are not automatically residents for 2023. If they want to be treated as residents for 2023 they have to make the "first-year choice." Making that choice requires attaching a statement to their 2023 Form 1040 tax return. See "Statement required to make the first-year choice for 2023" in IRS Pub. 519 (page 11). The original question says that they have already filed Form 1040 for 2023, presumably without the statement. I don't know if the statement can be attached to an amended return.
The OP didn't say whether they took the standard deduction or itemized deductions on the Form 1040 that they have already filed. I assume that if they took the standard deduction, and they make the first-year choice, they have to amend to take itemized deductions.
If they do not want to, or are not able to, make the first-year choice, then I think we are back to the original question of how to amend an invalid joint Form 1040 to two separate Form 1040-NR MFS returns. That probably requires following the procedure in the Internal Revenue Manual for an "invalid joint election." As a practical matter, that procedure requires professional help.
