Distributions other than a return of excess contribution before the due date of the corresponding tax return (including extensions) are not allocated against any particular amount in the HSA. In HSAs there is no separation of the funds into various groups (other than prior-year excess contributions, current-year excess contributions, and other amounts).
The 6% penalty for an excess contribution not returned before the due tax of the corresponding tax return is assessed every year until the year the excess is corrected or the balance in the HSA drops to zero.
