Class 1A National Insurance contributions: Calculating Class 1A NICs: Amounts made good by the employee: Making good payments do not reduce earnings chargeable to income tax
NIM15201 explains what is meant by making good.
If a making good payment does not reduce the amount of general earnings chargeable to income tax (see NIM15205), Class 1A NICs are due on the same amount of earnings chargeable to income tax, i.e. the amount chargeable without any deduction for the amount made good.
For guidance on the NICs treatment of loan accounts, see NIM12016 and NIM16675.