I'm not sure if I'm being helpful here, as I'm jumping in to say the same thing slightly differently, in the hope that it will be clearer.
There are two separate issues here, which it is in Nothern's interests to muddle together and the OPs interests to keep separate.
The first issue is a civil matter; whether the OP's delay repay claims were valid, and whether or not the OP may owe Northern money. This may or may not be the case; the rules are complicated. Losing a civil matter in a County Court because a judge decided that, on the balance of probabilities, the claims were invalid can lead to, usually, a money judgement against you. The judge has no power to fine or imprison or create a criminal record etc.
The second issue is a criminal matter; whether, if the OP's delay repay claims were not valid, the OP made the claims deliberately knowing that they were not valid, or with such a lack of concern as to whether they were valid that demonstrates a dishonest state of mind. This seems vanishingly unlikely. For my part, making the claims based on publically available data regarding journeys made seems like a clear demonstration of an attempt to ensure that the claims were valid. Losing this matter in a Magistrate's court because a judge decided that it was beyond reasonable doubt that the OP was dishonest would lead to a criminal record and conviction / fine etc. If Northern's services really were habitually late then of course the OP could get into a muddle. As z444z said, even if the claims are not based on a valid minimum connection time, that's not at all evidence of fraudulent intent or state of mind (and I assume they are based on a valid MCT, otherwise I assume they'd have pointed this out in the letter). Northern (like all operators) advertise with statements such as "If your Northern train has been delayed or cancelled and you arrive at your destination station over 15 minutes later than planned, you could be entitled to train ticket compensation through our Northern Delay Repay scheme." They also indicate that they will check claims, and advise that they will request more information if it's needed. An OP with honest intent and an honest state of mind could therefore easily think that if he arrived 15 mins late because his Northern train was delayed, he could be entitled to train ticket compensation, and that Northern would check his claims and let him know if they needed more information.
The OP should absolutely not attend the meeting; correspondence is absolutely the way to resolve this matter. The OP should start the correspondence by stating that at the time they made each claim they believed it to be valid, and that they are happy to help Northern understand each claim to the best of their recollection in order to help them check them. The OP should advice Nothern that they will be in a better position to provide useful information to help them via correspondence, as it will allow the time to provide considered replies checked against any available sources of reference information. (Normally advice might be to engage less, but I think in this case the potentially justifiable appearance of fraud means that it's better to both be and appear to be co-operative. This appears to be less of a fishing exercise on Nothern's part than, for example, some of the truly disgraceful e-mails Greater Anglia was sending out.)