Things like the DMCA provisions forbidding working around IP protection mechanisms (and software is copyrighted) don’t apply here.
IANAL (so take this it with a pinch), unless the trains are legally theirs rather than the train company’s, it’s not hacking, it’s just “software maintenance” and the only right this company has here is to withdraw product warranties because of “unauthorized changes”.
There might or not be a case against the train company (for example, if the contract forbade this or the train company tried to sell those trains onwards as if they were original) but not against the people who did the software changes on the trains when authorized by the owners of said trains.