Is it clear they have a reasonable claim for the whole journeys, when Milly's tickets for A-B and T-Z were valid? Perhaps unsurprisingly, National Rail Condition of Travel 13.4 means that travelling beyond the printed destination doesn't invalidate the ticket:
"If you travel beyond the destination shown on the Ticket, you will be treated as having joined the train without a valid Ticket for the additional part of your journey."
We are unable to find your requested journey at this time. Please try and select an alternative route or operator. Thank you.
www.nationalrail.co.uk
Milly, do you mean £400 covers anytime return fares for the whole journey?
They have little reason to think you went to London on your days off, if you tell them your job is Monday to Friday.
Although they may look favourably on your admitting the other weeks, they might still suspect - not entirely unreasonably - that you avoided full fares at times before that, perhaps further back. So the more records of payments you have (and/or evidence supporting the claim that you have only just started to travel regularly by train) the better.
There may be another aspect to your just starting work. If you've been working for three weeks and avoiding fares all of that time, they might reasonably think you could have gone on doing it long into the future, even when any factors you presented as mitigating no longer applied. It might be something to bear in mind when communicating.