Unoperable diesel engine

What is the proedure for isolating a defective unit in a consist?]

This site should help. A lot of locomotive manuals describing operating procedures. The answer to your question is in there. Very technical though, I’m not sure if thats the kind of answer you are looking for.

http://www.rr-fallenflags.org/manual/manual.html

trow isolation switch in isolate.
center the reverser so Tm can not act like generators.
and shut everything down.