Not 100% sure , but I think you could still buy a Hull Trains only ticket for one of there services yesterday from an LNER station booking office even though they would know about the disruption that Hull Trains was having and the arrangements for passing there passengers on LNER trains.
I bet also Trainline was still selling tickets for Hull Trains only services too yesterday and agin today I bet.
They all will be as they are in the system, you sell the passenger what they want. In this case i'd like to think that staff at a booking office would try and advise about potential issues though.