"We can't allow your claim for Health Savings Accounts you file F8889 HSA Adding $6,300 while eliminating AGI in the 1040x for the same amount. The computation does not match."
That statement makes no sense. Presumably you had family HDHP coverage, otherwise a $6,300 contribution would be in excess of what is permitted. Since you used TurboTax to prepare the amendment, TurboTax would not have permitted you to report an excess personal contribution on Form 8889. Assuming that a personal $6,300 HSA contribution was permitted, including this contribution should reduce AGI by $6,300. Your amendment would have included Forms 8889, 1040-X and Schedule 1, and your explanation should have indicated that your originally filed tax return failed to include the personal HSA contribution made by the deadline. If your amendment included these forms and the Schedule 1, it seems that someone at the IRS has made an error and you'll need to dispute this with the IRS. Perhaps they incorrectly disallowed the HSA contribution for some reason.
