I wonder if that behaviour would disappear if you ungrouped your station from your stops.
Un-grouping the stops did indeed prevent the bus line from altering with the modification to the rail…
Since noticing this behaviour I have been able to use it *somewhat* to my advantage by adding a signal, toggling it a few times and bulldozing it as a way of changing a lines path.. it doesn’t always work, but it has proved very useful.