The Chief Magistrate's decision seems to suggest that the 'bar' on prosecutions only applies for a short period whilst the Penalty Fare appeal is actually being decided, and not after that - whether the appeal is successful or not, and whether the Penalty Fare is paid or not.
However, many legally qualified people are doubtful of just how legally sound that decision is - and it is not binding, so it would be open to challenge if you were to find yourself in that position. In practical terms, the train company will not be interested in prosecuting you over this incident, since you have paid the Penalty Fare.
If you had shown an eTicket that was somehow invalid, e.g. you applied a Railcard discount but couldn't show a valid Railcard, then it's possible the train company would contact the retailer to ask for a list of your previous purchases. They might then go through those with a fine-toothed comb to see whether they were legitimate (e.g. if you had previous Railcard-discounted tickets, they might ask you for proof of holding a past Railcard). But that was not the case here, and in any event it would not directly relate to the journey which led to the Penalty Fare - that particular journey is closed as far as they are concerned.