I have build an trainnetwork that works by placing Trainstops before the Subway so I can route my trains through the entire network.
Trains need obviously need fuel so I made one station on the Surface for that purpose. Onto that I made an interrupt to get the train for every subnetwork that they are in to the Refill Station.
The Problem ist that the interrupts make temporary stations and those gets deleted by traveling beween surface and underground. (Dont know if that happens when traveling between 2 diffrent layers, but I would guesse that will happen there too)

Could you send me your savegame (without all other mods)?

From what I could test now, you have to plan your entire network carefully. Interrupt stops should be in each subsurface. Because if in the wrong subsurface, the train stops with no path.

But temporary interrupt stops aren't deleted when traveling.

I created a world where I replicated what I want to do. You can devide the railnetwork into 4 Subgrids (3 overworld and 1 underground grid)
The underground grid is for connecting those overworld grids.
The probelm is: I solved the refill problem with inerupts that trigger if the fuel is under an specific amount.
the real problem starts if the train is in the overworld. It will get the interupt and create temporal stations that are insertet cause of the interupt. if it then drives trough a underground rail it will forget those interupt temp stations and want to continue the next station like the interupt didnt happen.

my save file (didn't know how to send the savefile here)
https://drive.google.com/file/d/12vWIQA_wopxtiqr7EUwhgG6hVfL-WedF/view?usp=sharing

Figured out the issue, will be fixed for the next releaes