I don't have the knowledge to comment on whether there is, or might be, a viable defence to the underlying offence, so will refrain from commenting on this.
I'm not aware of any cases where a TOC has attempted to cancel a PF and prosecute *solely* for having appealing against the PF, provided that the PF was paid in full by the deadline.
For what's it's worth, I think that to cancel a fully paid PF and proceed to prosecution *solely* for exercising a statutory right, in this case, the statutory right to appeal against a PF, would indeed be an abuse of process, in that it effectively obviates, or renders ineffective, a statutory right granted by Parliament, contrary to the clear intention of Parliament (and the Government) that passengers issued with a PF should have a meaningful right to appeal.
Furthermore, a PF is a fare charged for travel, albeit one at a higher rate than normal, and payment of a fare represents consideration by the passenger for a contract to travel. This being the case, there might also be an additional argument that by choosing to issue a PF rather than proceeding to prosecution, and by accepting full payment of the PF, there is an implied term in the resulting contract for travel (albeit a contact for travel at much a higher fare than normal) cannot then subsequently be unilaterally repudiated by the TOC in the absence of any misrepresentation by the passenger.
It would be a very different matter if the PF was not (or did not remain) fully paid by the person to whom it was issued (so the contract for travel was not accepted), or if new evidence came to light suggesting that the passenger had deceived the RPI or TOC in some way, causing the RPI to come to a decision to issue the PF based on this deception (so the contract is void, or voidable, for misrepresentation).