As the title says , the mod will not call in any trains if trying to replace the vanilla locomtive with the pyanadon advanced locomotive.
I have bobs logistics installed at the same time, using its mk2 train works completly fine

Pyanodon's locomotives are all different sizes. mk2 locomotive is 7 tiles long. Vanilla is 6 tiles long. Train Upgrader is designed to replace rolling stock that's the same size.

This has come up recently, and it looks like they also adjust the spacing between wagons. It's possible that at some point I will try to update Train Upgrader to do something with the spacing in between cars and try to handle the case where the locomotive size is different but it works out the same with spacing. But for now it's checking the size of the wagon itself.