There are only three states that don't recognize HSAs: Alabama, California, and New Jersey...and Alabama is going to start doing so in tax year 2018 (i.e., right now).
I don't know of any adjustments needed for Indiana. Other things being equal, the state income reported in box 16 or whatever on the W-2 should be the same as the federal income...unless Indiana does something funny like not recognize 401(k) contributions - I have no reason to think this is the case, not knowing all the peculiarities of Indiana.
