I think your best bet is to file VT on paper.
You don't want to change the Vermont wages on your W-2 because that would indicate that they are taxable in Vermont.
You should file your Vermont return to get the $300 back that your employer should not have withheld.
I have not been in your position, but I have had clients that were in your position, and this is the best solution. And this way, your VT return will be accurate.
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