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It's fine. incoming medical students all of United States do the very same thing where they maintain a legal residence at their parents house while away for college.
Thanks for the clarification. I honestly didn't catch that he had moved to Massachusetts for employment I thought he was a student there.I agree that the OP will likely be okay, but not for this reason. College students matriculating to medical school is not analogous to the OP's situation. The OP moved to Mass. and established a household with full-time employment, which is not the same as a full-time student who has moved to a state for the express purpose of attending a specific school.
For clarity's sake, the legal concept that we're discussing is best called 'domicile'. It's nebulous because there is no recognized standard for when it's established. It's even more murky because it frequently becomes an issue only when one state believes it is owed taxes that were paid to another state, which is rare. However, in your case, moving to Mass. as a non-student with full-time employment is an overt act that demonstrates your intent (at least short-term) to live in that state.
I'm not that familiar with Mass., so what do you mean when you say that it takes 5 years to establish residency there? Having lived all over, all states with which I'm familiar require you to 'establish domicile' rather quickly, meaning you are supposed to register your cars, get a driver's license, etc., in your new state. I'm wondering if the 5-year thing is that Mass. will not grant you in-state tuition unless you've been a resident for 5 years. This is a relatively common tactic to keep people from gaming the system, but it's not the same as the state claiming that you are not yet its resident.
When you filed your state income tax return with Mass., did you do so as a non-resident? You probably shouldn't have because - again - for legal purposes you should have been considered a resident of MA. If you were trying to maintain your NY residency, then you should have filed in MA and in NY. Most states will credit you for the taxes you've paid elsewhere for work performed elsewhere, but I'm not familiar with the specifics of NY State's tax code.
The reason you'll probably be fine is because the people at your NYS medical school probably aren't savvy enough to 1) understand these concepts, 2) uncover the specifics of your situation, and 3) care enough to deny you in-state tuition. It helps that you have a long-standing history in NY and an in-state address, which helps explain why they'll never figure it out. It would help you to register to vote in NY, if you haven't already done so.
BTW, states don't issue passports, so that's not relevant.