When checking the box "my spouse is a nonresident alien" you should be able to file electronically as long as you are using the Married Filing Separately (MFS) status.
You will need to continue past the warnings regarding the missing information. If the return doesn't transmit, or is rejected, you will then need to print.
When the tax software does not allow for electronically filing of the NY return, the state will accept the printed/mailed return, if you end up needing to mail the return.
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