I will assume for the sake of argument that the train operator has accurately calculated the undiscounted fares for journeys where the wrong railcard discount was claimed, and that there is no basis for claiming that journeys have been included in the calculation for which the correct fare was paid.
I do not see a basis on which the OP's daughter can apply a discount to the sum claimed by reference to the fact that she held a 16-25 Railcard. On the basis of my assumption above she did not claim the discount made available by that railcard for any of the journeys forming the subject of the claim at the time of ticket purchase, and cannot do so retrospectively to reduce the measure of the operator's loss.
My understanding of the operator's case is that that the undiscounted fares for those journeys amount in aggregate to £1,616 and that the OP's daughter claimed a 50% discount on those fares by falsely representing that she was eligible for such discount by virtue of the 16-17 Railcard she held. On that basis the implication must be that she actually paid the operator sums totalling £808 for the journeys concerned. The fact remains, therefore, that she has made payments to the operator for the journeys giving rise to the claim, so that the actual loss of fare income suffered by the operator is the wrongly claimed discount of £808.
The operator's solicitors appear to be approaching this as a claim in contract, judging by their reliance on NRCoT. I think it could equally be approached as a claim for the civil wrong of causing loss to the operator by misrepresentation (that the OP's daughter's was entitled to a 50% fare discount as a 16-17 Railcard holder and remained within the eligible age range). But in either case the measure of damages recoverable must reflect the actual loss to the injured party, and credit should be given by that party for the fare income received from the wrongdoer for the journeys giving rise to its claim.
The expense to a claimant of investigating a claim such as this is, in principle, recoverable as a head of damages, subject amongst other things to such expense being provable as an actual cost to the operator concerned. The operator's 'Fraud Investigation Costing' contains some indications that a record has been kept of staff time spent on the matter, although the time expenditure being recorded as full hours suggests that it may not be backed up by detailed records of time spent, and is thus open to challenge. 'Case Processing Costs' of £150 likewise appears open to challenge, and the response should request details of the documentation supporting the claim for these expenses. If they cannot be substantiated as an actual cost to the operator, it is likely to recover no more than a nominal sum for these as a separate head of damages.