Yes, Meg, I believe that you are right that it was an illegal deduction, and it canot be retrospectively applied either.
What has happened is that your partner's employer agreed T&Cs of employment with your partner for one thing and now wants to change it. They can do this legally, but not without giving notice. Unless his contract says anything that defines it as longer, then I'm afraid the notice period is only one week.
Unfortunately until your partner has not been there for 12 months, the person is not covered by the unfair dismissal legislation (OK so there are some exceptions - pregnancy for example!). So he runs the risk that if he fights it, they could decide that they no longer want his services (again at one weeks' notice, or maybe longer if in the contract).
But as Zacmaster has pointed out, the employer should not be having to reimburse HMRC for the benefit provided by the van anyway - suggest he refers them to the sheet Z found - and try and get them around without losing the job. HTH