Yes, your refund will be based on how much of your wages were earned in Maine.
If you look at your W-2 form, you will see your state information in boxes 15, 16 and 17. Based on what you are saying, I'd expect to see a line with Maine wages and another line with New Hampshire wages. The total of the two should add up to your total wages.
You will be taxed as a nonresident in Maine on the wages listed as Maine wages on your W-2 form.
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