I've no doubt that a significant number of people will be caught 'fair and square' through this initiative. And if so, it's quite right that they should have to repay the refunds they have illegitimately obtained.
However, I have three main concerns:
1) Some people will have legitimate reasons for claiming a refund even though their ticket has been scanned.
If they passed through the ticket barrier before realising the train is delayed or cancelled, their ticket would have been scanned even though they didn't travel.
And indeed, passengers can quite legitimately abandon their journey part way through and return to their origin, if there is disruption en-route. They would still be entitled to a full refund in this case.
Based on the past behaviour of TOCs' prosecutions departments, I don't necessarily trust them to accept an explanation as above. It's quite possible that people would be told that they will still be prosecuted regardless of what they say.
That, of course, also assumes that people are given sufficient detail to work out what journeys the letter is referring to. The letter we've been linked to doesn't give any detail at all.
And even if people are told (or work it out), if the letter refers to journeys that took place more than a few months ago I think it would be difficult for most people to recall exactly what happened. We saw this with the Greater Anglia Delay Repay "fraud" thread, where people simply can't say exactly what happened on a random journey a year ago, so felt they had no choice but to settle out of Court.
2) Some people will have claimed a refund in error, e.g. because the train was delayed and they were told they could "claim money back".
Lots of TOCs' customer services and frontline staff don't seem to know the difference between a refund and Delay Repay - so customers can hardly be blamed for confusing the two.
Again, where this is the case, I wouldn't trust prosecutions departments to play ball. I could quite imagine them saying "you would have been entitled to Delay Repay, but because you claimed back through the wrong mechanism we're prosecuting you".
3) Overall, this has strong echoes of GA's Delay Repay fraud intiative. Whilst, as there, I'm sure they are catching people who are in the wrong, a blanket £90 "admin fee" seems unlikely to represent a true approximation of Northern's costs. I suspect it is (and is intended as) a thinly veiled penalty.
It also seems wrong that, when Northern are making an accusation as serious as fraud, and in the same letter offer a bribe settlement to avoid legal action, they do not give exact details of their allegations. I would also be interested to know in what percentage of cases they actually intend to take to Court if the settlement isn't paid. A prosecution for fraud requires strong evidence and isn't a 'run of the mill' prosecution as with what TOCs often have sessions at Court for.
Overall, I think Trainline need to improve their refund processes - it needs to be much clearer what you are requesting and what this means in terms of the validity of your ticket, and potential criminal liability if you request a refund where you are not entitled to one. The industry also needs to brief every single customer facing member of staff on the difference between Delay Repay and a refund. It is unacceptable that there is such a lack of clarity when the industry is able and willing to prosecute for fraud.