The IRS does not have your Indiana tax return; the Indiana Department of Revenue has it. So the IRS has no reason to hold any refund from a tax return that they haven't seen.
And the Indiana refund (if any) for 2018 probably will not be held up if the letter is about an earlier year (i.e. 2017 or before). But if the letter is about 2018, then your current refund (if any) will most likely be held up until you answer that letter.