When settlements are reached within as short a period of time as two weeks of a Hearing listed in a Magistrates Court, then a Summons will have been issued, and so there are by that stage three parties involved : the accused passenger, the prosecuting officer from the Railway Company, and the Clerk of the Court. All correspondence should always be between all three parties.
I will guess that you and the Railway Company made an agreement (which was presumably honoured) but that neither of you informed the Court, or, that if there was any delay in honouring the settlement, then by the time that the Court were informed, it had gone forward for Hearing anyway - a Hearing which you didn't attend, and at which you don't know what the Railway's Prosecutor said (who would have been there anyway for other similar matters being heard at the same time).
In my opinion, it is the Court's Clerk's office that you should be speaking to, as they appear to be the party who needs to be informed. It will still be for the Railway Company's Prosecutions department to contact them as well, to confirm that the case was not being pursued, and you will also have to contact them to ensure that they are satisfied that your agreement to settle was honoured and that they would want to withdraw the Prosecution against you.
But just to be clear, where a Summons had been issued for you to appear, then you should appear - whether you had reached a settlement or not. A Summons is an important order not to be cast aside without sound reason which is confirmed by the Court which issued it. When you speak with the Court Office, you can ask them to clarify what is written on the summons thaat you are being asked to answer to, so that you know what to say to the Railway Company when you speak with them later.
I can't agree with the responses above that it matters which Company it is, nor whether you were travelling in First or Standard Class, nor whether the Railway Company is considered 'stupid' by some on this forum - this question can be answered fully in terms of straightforward Court procedure and if a settlement has been agreed and honoured, then it no longer has anything to do with rail travel.