On the first list, you should have been able to click on "None of these apply to me". I don't know why this put you in a loop, but it looks like you found a way out.
Your justification looks fine; honestly, it doesn't have to be real detailed - you mentioning the 8889 is good.
Yes, you are able to file/amend only the federal return, with one LARGE exception. Some states require that you amend the state return if you amend the federal return. This is because changing the federal numbers might change your state numbers.
If the change to the 8889 changes your AGI on the 1040 then I would say, yes, you need to amend your state returns. However, if none of your federal numbers change, I would encourage you to contact your local state tax offices and ask them. This information is not easily found on their websites.
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