The new tax code will tell their PAYE system to amend the tax it takes from him, but as tax is calculated over a whole tax year, he will not see a big sum rebate for the "overpayment" so far this current tax year.
The overpayment so far this year will not be taken into account in this new code, but should be allowed for in next years (once they know just how much he has/hasn't paid in tax for the WHOLE tax year). A rebate is only payable if they can't adjust your code enough for you to pay less tax to cover the overpayment for the rest of the year. After the end of the current tax year you can apply directly to the tax office for a rebate if you feel you paid too much this year.
Rebates, generally, can only be made once a tax year is complete (assuming there is still an overpayment), not whilst it is running (so based on a previous tax year,not the current one). It could be that he earns more, or less during the balance of the tax year, so the final calculations can only be done knowing what he HAS earned, not what he MIGHT earn. If he does pay too much tax during this whole year (even with the adjusted tax code) then his code for next year should redress the balance.
I'm run a small company with just a few employees and this tax stuff can really do your head in sometimes!!