When calculating tax, unless there is a M1/W1 (Month1/Week1) indicator, it takes the total paid for tax (including this pay period), removes the total tax free pay (including this pay period) and calculates the tax on the result; the total tax paid so far (to the previous pay period) is subtracted from this and the difference is the tax to pay, capped at 50% of his gross pay.

(If there is a W1/M1 indicator, it subtracts one pay period tax free pay from his gross for tax in this pay period and works out the tax on this.)

I would suspect that through the period when you were reducing his gross, the total tax free pay to date was catching up with the gross for tax paid to date.  However, in repaying the gross, you now reset his gross back to what it should be, in which case his pay has a large jump relative to the tax free amount.  There is a statutory limit of 50% of earnings that can be taken as tax (I presume to try to prevent poverty in the lower tax bands)).

The question I would ask is did you process his repayment of the excess gross¹ through the payroll?  If not, when you returned to the normal gross pay, the total pay would include the excess gross paid in error that has not now actually been paid (and he received less tax and NI).

To check what tax (and NI) he should have paid if the overpayment had not been made, I would suggest:

1. Note his total tax and NI at the moment
2. Take a backup of the payroll data.
3. Rollback the employee to the period of the overpayment.
4. Re-run the payroll for each period with the correct full gross (do not send FPSs², just print his payslip (if you want) and update his record)
5. Note his total tax & NI that should have been paid.
6. Restore the backup².

You should now be able to check his total tax and NI paid and see if they are correct.

¹Do you really mean repay the Gross overpayment from the net pay he had received?  The net pay is less tax & NI. If he has repaid the full outstanding gross (from his received net pay), then tax and NI will be taken from this pay twice: once when he received it the first time (erroneously) and again when you give it to him properly.

²You're not trying to correct anything (possibly, yet), you just want the information about tax and NI for the moment, hence why the backup and restore.

When calculating tax, unless there is a M1/W1 (Month1/Week1) indicator, it takes the total paid for tax (including this pay period), removes the total tax free pay (including this pay period) and calculates the tax on the result; the total tax paid so far (to the previous pay period) is subtracted from this and the difference is the tax to pay, capped at 50% of his gross pay.

(If there is a W1/M1 indicator, it subtracts one pay period tax free pay from his gross for tax in this pay period and works out the tax on this.)

I would suspect that through the period when you were reducing his gross, the total tax free pay to date was catching up with the gross for tax paid to date.  However, in repaying the gross, you now reset his gross back to what it should be, in which case his pay has a large jump relative to the tax free amount.  There is a statutory limit of 50% of earnings that can be taken as tax (I presume to try to prevent poverty in the lower tax bands)).

The question I would ask is did you process his repayment of the excess gross¹ through the payroll?  If not, when you returned to the normal gross pay, the total pay would include the excess gross paid in error that has not now actually been paid (and he received less tax and NI).

To check what tax (and NI) he should have paid if the overpayment had not been made, I would suggest:

1. Note his total tax and NI at the moment
2. Take a backup of the payroll data.
3. Rollback the employee to the period of the overpayment.
4. Re-run the payroll for each period with the correct full gross (do not send FPSs², just print his payslip (if you want) and update his record)
5. Note his total tax & NI that should have been paid.
6. Restore the backup².

You should now be able to check his total tax and NI paid and see if they are correct.

¹Do you really mean repay the Gross overpayment from the net pay he had received?  The net pay is less tax & NI. If he has repaid the full outstanding gross (from his received net pay), then tax and NI will be taken from this pay twice: once when he received it the first time (erroneously) and again when you give it to him properly.

²You're not trying to correct anything (possibly, yet), you just want the information about tax and NI for the moment, hence why the backup and restore.