Clearly, there are some things - probably fewer than there once were with the arrival of computers - where ultimately, only the defendant knows the answer. Once upon a time, the example always given for training purposes was third party insurance. If the police have some proper reason to want to see it, and for some reason the defendant never produces any or an exemption, then in the end the only answer is a summons. It would be impossible for the prosecution to prove that no insurance existed.
In general, and I've never heard it suggested that traffic lights, or the police directing traffic is any different, it is up to the prosecution to prove a case 'beyond reasonable doubt'. Now, a police officer giving evidence that they had seen the defendant riding through red traffic lights which were working correctly would, on its own, be compelling evidence. In fact, the officer's evidence would also include any interview he conducted when he stopped the defendant. Bearing in mind that the caution now includes the bit about mentioning now things relied on at court, it might be reasonable to expect our cyclist to point out that he had been directed to ignore the traffic lights by another police officer. (For a successful prosecution for failing to conform with the traffic light, a notice of intended prosecution would also be required, at the time or within fourteen days.)
Once the allegation had been made about the police officer directing traffic to ignore the light, a prosecution file would have to cover the point. I cannot see a prosecutor going into court with a file without knowing what evidence was available on the point. It's my impression that the Crown Prosecution Service is more circumspect about accepting police evidence than might have been the case previously. Depending on the circumstances, I find it hard to see how the case would be taken unless the reporting officer - who must have had a clear view of the lights to report anybody for riding through them - could say they could clearly see that there was no other police officer there directing traffic or, another officer who was on duty by the junction gave that evidence. In other words, if the cyclist's explanation could not be rebutted, I think the case would never get to court.
If the case did go to court, and if the defendant were to be properly represented, it would be one of the first things the reporting officer would be cross examined about. (In legal terms the evidence of witnesses is assumed to be accepted by the other side unless challenged by cross examination.) At the end of the prosecution case the defence might make a submission of 'no case to answer'. Unless the prosecution had satisfied the court that there was a convincing case, the matter would stop there. If the court did not accept the submission or if none were made, the defence could call the defendant and as many other witnesses as they felt were helpful. If the defendant gave evidence that he had been directed to pass the light at red by the police and that is why he had done so and if he continued with that explanation when cross examined it would be a matter for the court to decide bearing in mind that the onus is on the prosecution to prove the case beyond reasonable doubt. All the defence has to do is raise a reasonable doubt. This is something that I don't think has anything to do with the balance of probabilities.
I do know that anybody who is convinced that the entire legal system from the Lord Chief Justice down to a process clerk is corrupt and all the rest of it will believe that everything is decided in spite of the evidence. I cannot help that.