not quite sure what you did. interest from EE U.S. savings bonds is taxed at the federal level but not at the state or local levels for income tax purposes.
it seems you filed amended returns correctly by filing only for the state.
However, if you used the bonds to pay qualified education expenses the interest may also be exempt for federal purposes. see this link
https://budgeting.thenest.com/redeem-savings-bonds-paying-taxes-33036.html
