We are seeing quite a few cases like this where, after the original case is settled, the train company then comes back for another bite of the cherry having discovered other suspicious transactions.
My own view is that the train companies should carry out these further investigations at the same time as dealing with the original case.
The OP has a choice here:
1. They co-operate with WMT, and pay a further settlement to be certain of keeping the matter out of court.
2. Say nothing. Purchashing rail tickets with a discount you're not entitled to is not illegal, using them is. It would be near on impossible for WMT to prove beyond all reasonable doubt that the tickets were used by the OP illegally for travel. A prosecution under the Regulation of the Railways Act or Railway Bylaws would almost certainly fail. There is a small possibility that WMT could try and prosecute under the Fraud Act.
There is the possibilily that WMT might have sufficient evidence to prosecute under the RoRA or Bylaws. They might present a case to the BTP who may, in turn, ask the OP to attend an interview and generally make life difficult. They might try and prosecute, try and get the OP to plead guilty, and withdraw if the OP turns up to defenf themselves.