I'd want to know - did this occur in two different plan years? If so, then the participant got credit for the taxes that were paid in to the IRS on his behalf. That amount (which would have been reflected on the 1099-R form) went toward his overall total tax debt.
Even if the distribution occurred in the current plan year, the participant would still receive credit for those taxes paid into the IRS on his behalf so I would say that the participant would have provide 100% of the distribution amount back to the Plan.