https://mods.factorio.com/mod/Train_Control_Signals automatically inserts and removes a custom icon (the green one) in schedule stop names in order to skip them. This causes the Railway Controller to think the train's schedule was manually changed and is no longer part of a Line.

This could be resolved in a hard coded way specific to that other mod, or maybe it could be resolved by adding a mod setting for this mod where the user can put characters / icons / strings that should be ignored when comparing station names to determine if a train still has the same schedule.