Is there any way to disable custom liveries on timetable mode? I've installed some Heathrow Express and GWR liveries for the 387 and 395 for a scenario in GWE. However, these trains are now showing up in SEHS and BML.
No, there currently isn’t a way to disable liveries in service mode. They’ll appear at random wherever that certain piece of stock shows up. This needs to be a feature. I’d personally rather keep custom liveries exclusive to custom scenarios.
If you are PC user then yeah you can disable liveries with command (you can place it into the ini file). If you are console player then you are out of luck - there your option is only delete those liveries.