And then what? The train just stops in the middle of nowhere for however many days until the one chamber is fixed?

It returns obviously. Making repair or replacement of damaged sections economical is one of the engineering challenges. This by itself suggests compartmentalizing along the same lines I suggested.

It would probably be ideal if you could factory make each section and ship it on a standard truck, but with the growth of additive manufacturing, other possibilities also open up, like 3D printing the large metal container onsite.

I think you'd have to print it onsite, otherwise you have no gain in the loop being underground as you'd have to dig basically the entire ground up to swap sections.