You must file MD to receive your refund since you live in PA. You can file your PA jointly, because you must pay the tax to PA since you are a PA resident. Your PA tax will not change on a joint return because all of the income for both of you is taxable. As you know they use a flat rate.
In TurboTax you need to do two things; first file the nonresident state return of MD for a full refund. TurboTax knows this is a reciprocal state for a PA resident. Next, file the PA return as full resident for each of you separately or together.
When the returns are filed through e-file, MD should know to release all of your refund. If necessary you can mail the MD return with a copy of your PA return as resident. Be sure to mark the MD return as a nonresident.
@Zachary0301
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