If your NY MFS tax return is sent with the same account as the Federally Filed MFJ return, it probably will be able to file and accepted electronically. If not, TurboTax (and NY state) will let you know accordingly.
Your spouse's MFS NY return will need to be mailed because it is "detached" from your Federal MFJ return, because you are using a separate account to prepare the mock return.
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