This bug was reported on Steam after the 123 release, but I was busy back then and the bug was not reported properly, so I eventually forgot until I suffered it myself this past week.
QuoteSince the patch I have problems with editing vehicle lines. I can no longer set free waypoints or they are not saved. When I change a train line, the affected train suddenly has no line anymore.
You need to edit the line from a vehicle details dialog. In my experience, the line is indeed changed correctly, but after the edit the vehicle has no line any-more and doesn't include the changes done to the schedule.
That is tricky to solve. A similar thing would happen, if a schedule tab is open and then the line is edited. I will see how to change this.