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State tax filing
It's really hard to know what you did in those years, such that TTX might have indicated that you had to file nonresident MD taxes...whn..in fact, you didn't.
One way TTX "might" have prompted you to file MD taxes, is on the initial My Info page.....in there you "might" have indicated you worked in another state. If you entered "MD" in there as another state you worked in, then TTX would have told you to file MD nonresident. But, in your situation, you should only have done that in the years that MD taxes were withheld.
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An additional comment...for the years that you amend MD to get the improperly paid MD taxes back, you will also likely need to amend MA too......since you probably claimed a MA credit for taxes paid to MD in each of those years. What should end up happening is that you'll get some MD taxes back, but then have to pay those same $$ back to MA as a part of the amended MA tax return.
I have no idea if MA will assess a penalty or interest on the taxes you should have been just paying them over the past couple years, due to the improper credit for taxes paid to MD..... But just remember to start with the earliest year, and mail in each year's amendment separately. And it could get complicated enough, that you might end up needing to use a local tax professional instead.