How much would you chase HMRC?

A client of mine is winding up his business and closed his CIS records about 6 months ago. When I was checking his records I realised that there are two instances where he'd correctly deducted CIS from subbies but hadn't declared them on the CIS returns or paid HMRC. He phoned the CIS helpline a month ago to inform them but no-one knew what to do so they said they'd phone him back but they haven't. It's not large amounts involved - would you be chasing HMRC or has my client done sufficient already?
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Agreed. Though strictly speaking if the client owes the money (and indeed the subbie is going to claim that deduction on their own tax return) the money should be paid over with the explanatory letter. Don't expect HMRC to deal with it right though, they will probably bank the cheque and ignore the letter.
I've done something similar and my client paid, and now they have an "overpayment" even though they've been advised that the liability was due (Class 1A NIC on amended P11D as opposed to CIS, but same difference).