Well, if I understand you right, you filed the NJ returns way back when with no NYS credit for taxes paid (because you were unaware of this). Now you have filed the NYS returns, so you know the amount of tax to NYS (and NYC), so now you can take this amount as a credit on your 2017 and 2018 NJ returns.
In other words, it looks like you have paid both NYS and NJ state tax, so now you get to amend the NJ returns to take the NYS tax as a credit for NJ taxes.
Make sense?
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