I created separate mock federal and state returns in order to file the state tax return separately. But I efiled the federal return jointly. So when I try to e file my new York state tax separately, the system doesn't allow me to efile because I did not file the mock separate federal return
Yes, joint Federal and separate states requires the state be paper-filed and mailed. NY suggests the state be efiled, but this is an acceptable exception to that rule.
YOU DO need to include a copy of your joint Federal return.