Yes, you should be getting the Michigan tax withheld refunded since you do not live nor work in Michigan.
Why do you only get a partial amount back when you file a Michigan return? Are you allocating zero income to the state of Michigan?
Michigan taxes nonresidents on income only if they are physically present in the state.
Yes, you should amend the state returns if you are due refunds. Some states DID tax remote workers in the past but I do not think Michigan ever did. You can ask your payroll department and they would know if the tax laws changed for Michigan.
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