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The two stations with requester chests are of interest. Ignore the other three. I have two stations with identical names "iron output." In the past, when the train in the top right reached the blue chain signal, Factorio would see that it has a route to the right "iron output" station, and correctly proceed to that station since there's a green signal after the blue chain signal. Unfortunately, in present versions, the train is stuck trying to go to the left "iron output" station, causing a deadlock.
I think the major issue is that I have N stations with the same name, but N+1 trains assigned to use those stations. Both stations were occupied when the top right train departed, and the game just chose one of the stations. It proceeds as far as it can, but doesn't realize that the other station became available during its route. In the past, the game seemed to recalculate route when it got stopped at a blue chain signal, but that no longer works. If I toggle the top right train to manual and back to automatic, it recalculates the route and properly proceeds to the available station. That used to work without user intervention.
I attached my save file. I also added my mod-list.json to make it easier to load this save, but none of the mods affect train behavior.