On the basis that he was not working anywhere else from Jan-April then his tax credits for those months would be available against his employment. The tax credit cert may have been issued aon a "month 1" basis , i.e. from April onwards only, as Revenue were not sure of his status pre-April. It would hav no bearing on the employer status as semi-state. It might be possible, if he rang the Revenue helpline on the cert to have it amended to a "cumulative" basis. If they did that and it got in before the end of the year then the employer would refund any tax overpaid. If he doesn't get this amended before end of year then it would be adjusted on a tax return filed after the end of the year. He won't lose the value of any credits due to be taken into account.
For 2008 the cert should be on a cumulative basis.