Hi, I'm not sure which step was the problematic one, but here's what I did:

For each Trainbuilder of my 4 sections trains:
1 - Changed the requester chest from MK1 parts to MK3 parts
2 - Changed the recipe on the builder to make MK3 trains
3 - Mined the current train on the track under the builder

Then, since I have 3 depots associated with these, I mined the MK1 trains that were there waiting.

But the trainbuilders never spawned another train on the track and the depots train limits were marked as "0/None".

Removing the trainbuilders + controller and building them again made them start working again.

Just to be clear, the trainbuilders did go through the process of building the train inside the building, but they were never put on the track.

As mentioned before, I only had to mine the builders + controller and place them again and then it was working again.

I just remembered that after I removed the builders, the cargo wagon ones had their inserter with trainfuel on the hand that I had put on the chests by mistake.
So now I'm not sure if I had done this before the new parts arrived or not, I thought I had opened all builders to check if they had built a train, now I'm not sure.
This might have been 100% my mistake and not a bug.

When you removed a recipe, the controller should be 'destroyed' if it was building a train. If it was dispatching a train, it would not. When you copy paste a recipe, it should've deleted the train on the tracks and start building the correct train. I don't see any way how this would get the builder stuck in any unknown state. I do believe it was building a wagon at the time, or had missing ingredients when you removed the whole setup and rebuild it...