I'm playing with game version 1.0.0 and use FatController and Smarter Trains at the same time.
My issue is that the Train Line deactivates itself after some random time and the normal scheduling is continued.
Maybe I'm missing something.

The interesting part is that the Deactivation is not sensed by the GUI. I have to close and open the ST UI to actually see that it happened.

Ok. I could fix it by myself. A friend told me to check all my other mods for train related changes.
This mod is not compatible with "Wagon Auto Graphics". I assume that the Cargo wagon objects of some sort are replaced in the game and this leads to the deactivation of the Train Line.
This issue might be interesting to others and maybe to avoid this in the future for other players this mod should detect "Wagon Auto Graphics" and then print a warning.

I haven't looked at the code yet, but this sounds like I will need a savegame. Can you upload one where you are in a train that is still assigned to a line?
Normaly lines don't get unassigned randomly (only when you add/remove waggons or locomotives i believe). I'll have to check the code tomorrow to ne sure though, haven't used SmartTrains in a while.

Yes, that mod is the issue. There is currently no (easy) way to fix this. Perhaps i can find some quick hack, but since SmartTrains needs a rewrite anyways I'm not ging to spend a lot of time on it.

I'll either show a notice, or mark it as incompatible, since it likely breaks almost everything SmartTrains does.

Edit: No need for a savegame ;)