Out of interest, now that you've had the matter fully resolved/closed, on reflection, do you think that you might have taken the odd advantage on occasion and tried to get away with it? I know you say "memory problems", but must have been on a few occasions to flag!
No judgement, and you seem to hold your hands up, but essentially, I think some forum members would benefit to know that the train company isn't just going round picking on people just to make money, and they do have some substance to their case!
No idea what that train company is - but I find it hard to believe that any reasonable and frequent commuter wouldn't be aware of changes such as that. Certainly in my season ticket days I was pretty clued up to the best trains/seats/routes and my rights!! In any event, surely it is your own responsibility to read the relevant terms and conditions before purchasing your ticket?
Also, surely, worst case, you'd realise after your first renewal, e.g. a week or a month? So worse case you've not been able to claim compensation for some of the previous month, (but I think you get 28 days to claim anyway, so with a monthly ticket expiring, you could still potentially claim back 28 days prior, if you found out literally when buying your next ticket?)
I'm not sure of the precise arrangements in your circumstance, but if you had an annual ticket, I am quite sure (certain) that only the most ignorant person would wait 12 months and not realise any arrangements had changed. Worst case it might take a month or two to realise, during which time you might only have had a couple of delays anyway, not amounting to all that much.