Oh, not this chestnut again!
We had this issue when CrossCountry started selling their anytime tickets, people kept buying them because they were cheaper than off peaks and TPE and EC staff were getting all sorts of abuse when the punters were told, no good, you have to buy a new one.
Route specific tickets can be upgraded by an excess, so say manchester to leeds via hebden bridge isnt valid on a TPE service via huddersfield as TPE dont run bia Hebden Bridge but can be upgraded to allow the huddersfield route. Regardless of the fact only NR run via hebden bridge, it is route permitted to use TPE leeds to Huddersfield then change for a service to halifax and on to the calder valley. So the revenue is still shared by both operators, but via hebden bridge northern receive a greater share whereas any permitted TPE get the bigger share as their 5 trains vs northerns 4 when changing stoppers at huddersfield or using the blackpool service is taken into account.
The difference with TOC specific tickets is that the TOC receives 100% of the fare, and not the RSP proportion shared with other TOCs on the same route. Therefore these tickets cannot be excessed as the operator that actually carries the punter doesnt receive any farebox for that ticket. I have this issue with people who buy grand central tickets, then travel on a TPE service, I cant accept them and I cant upgrade them. They will have to purchase a new ticket.
The analogy can be put like this. Basically, if you were taking a ryanair flight to say, paris. buying a flight ticket for easyjet wouldnt get you there because you paid easyjet the fare, not ryanair, so if you boarded a ryanair flight they would tell you to take a hike and buy a new ticket. Its unfortunately the same case with TOC specific tickets, in the same way as an advance purchase for an EC service cannot be used from York to Newcastle on an XC service. Like it or not this is one of the pitfalls of privately operated railways that we have now.
Its often the result of misreading the ticket machines and selecting the wrong ticket. In both cases i have highlighted here i reguarly come across this, and have to recharge accordingly. I understand why mistakes are made and am one of many people who are calling for a much simpler ticketing system than what we have now and i do feel for the people who have made genuine mistakes, but if i dont correct the mistake and charge accordingly, then if something goes wrong, the ticket holder isnt insured and would be entitled to nothing.