The warning comes as the ORR revealed that NR had reduced the number of delays caused by infrastructure problems - they were 9.8% down on the same time last year.
After receiving the fine in February, NR chief executive Iain Coucher said his company had put "military-style" command posts in place, and pledged the delays suffered by passengers over New Year would not be repeated.
Further, the letter notes, in order to defend itself NR would be entitled to seek discovery, and in the process obtain access to e-mails and other records that Mann has, thus far, resisted disclosing in various freedom-of-information suits prompted by ClimateGate.