Thanks for your reply.
The payroll is processed in FreeAgent and weirdly, having pension contributions set as 'Relief at Source' means that they are deducted from their net pay, rather than from their gross pay!
So they haven't received any tax relief since 2018; the full pension contribution has been invested, so it's just that their income tax has been overstated.
Assuming that they would have received the basic 20% tax relief, would it be reasonable to calculate this as the amount of tax overpaid?
I'm guessing I'm going to have to approach HMRC to try and resolve this, but Lord knows how long this will take!