Well, yes and no. It'll affect the EMP501 recon, but not the PAYE portion.

You can issue the IRP5 or IT3a, but when you do the EMP501 recon and put in the amounts per the EMP201s paid, there's going to be a shortfall. If you make that extra payment, it may be resolvable using payment allocation tools either in E@syfile or efiling. Or you might have to go into SARS...