Yes, you are correct. The same information that Mike9241 referenced in Publication 969 is also under "Deducting an Excess Contribution in a Later Year" on page 6 of the Instructions for Form 8889.
If I understand it correctly, you have to include the carried over excess amount (your $400) in your total HSA contributions on Form 8889 for the year that you make the adjustment, so you are actually deducting the excess amount in that later year. Your HSA deduction for that year will be the same as if you contributed the full maximum amount and did not have any excess in the account. It's not clear where you are supposed to include the excess amount. You probably just include it in line 2 of Form 8889, but the instructions are not clear about that.
Show your CPA what it says in Publication 969 and in the Form 8889 instructions. If they still won't let you do it, find another CPA.
