At the PCN stage, you can submit an informal challenge, and if they reject it (like they do for about >95%) of them, they re-offer the discount. To stop the matter going any further, you can pay this.
However, if you don't pay, your company will get a Notice to Owner. At this stage the discount is lost, so the company are now liable for the full PCN penalty. Your company may not even own the van, it may be leased, in which case the lease company will get the NtO. So as you can see, it is a bit of a Pot Mess. You need to find out what the company does for their workers getting a PCN and if the van is leased or not.