Jason, just a stab at what may have happened...
The line was built as the Black Hills & Ft. Pierre in 1881, and then the Deadwood Central came about in 1888. Both were taken over by the "Q" in 1904 and scrapping began in Dec. 1930.
The few pictures of any boxcars on the narrow gauge have no numbers until the "Q" took over. One shot in the afformentioned book shows the "Natalie" 0-4-0T (on display at Crazy Horse Monument) on the Branch Mint 3 mile line with a CB&Q gondola sporting the 5 digit numbering system taken in 1906. The only piece of equipment ever going to the C&S was Deadwood #5 ("Q" #537) and outside frame consol that was leased from 1930 - 39 and scrapped. It was said to have run Denver to Leadville, but its disposition is unknown to me. Maybe others can enlighten us.
Jeff