@Opus 17 wrote: "If you want to argue that she has changed her domicile to state B, then you need to file state A as married filing separately (MFS)"
That depends on the states. Some states require you to use the same filing status that you use on your federal return.
Most states still allow you to file Married Filing Jointly (MFJ), even if the two spouses have different residency.
Don't use MFS without comparing the net tax change of doing so.
What are the states? If they are reciprocal states, it could make a difference. Need to look at both states specific domicile rules. Although from what you describe, she is likely considered a resident of the new state. On the other hand, the family's primary residence is in the old state. Is her employer withholding for the new state?
All that said, based on what you have described so far, I would file a joint resident return for your state and a non resident return for her state. File the non resident return MFS or MFJ whichever works out better and is allowed.
