Having grown up in Los Alamos I seriously doubt the idea that the bottom end of the Chili Line remained intact after the rest was abandoned for a couple of reasons.
The Govt. was pretty detected to trucks at the time and would not have likely been interested in another USA narrow gauge operation.
The operations would have been awkward as there were no real facilities at Otowi.
The road form Santa Fe to Otowi was in pretty good shape so running a railroad over that stretch wouldn't have saved much(if any) trouble.
Los Alamos is one of the only National Labs that doesn't have any rail service, had the Govt. taken over the railroad they would probably standard gauged it and extended it up canyon a ways and it would still be there.
If the Govt. was running the bottom end of the Chili Line why was 478 used instead of one of the USA K-28s, and why wouldn't they have bought the coaches too.
An Army General was in charge of construction and had all the motor resources of the US Army at his request, there was no need for a railroad.
Lastly, the time scale is all wrong, the Chili Line was abandoned in '41 and Los Alamos didn't really get started until Aug. '42 and the lab didn't open until '43.
This sounds like a myth in my book, but as I have no proof I can't say that it is wrong.
Paul