To answer your last question first, yes, the Soo Line has been merged into Canadian Pacific since 1992, but the CP hasn't repainted all the engines yet. In fact, the last time I passed by Bensenville Yard in Chicago, the CP was still using some orange-and-black former Milwaukee Road switchers, and the Soo bought the bankrupt Milwaukee in 1985!
The Soo's early diesel switchers and road switchers were black with imitation gold lettering. The maroon and gold colors were introduced on Electro-Motive F units and also used on GP-type road switchers in the 1950s. In 1961 the Soo Line adopted the red and white (actually a very light gray) colors with the big "SOO" lettering. This marked a corporate restructuring in which the Minneapolis, St. Paul, & Sault ("Soo") Ste. Marie, Wisconsin Central, and Duluth, South Shore & Atlantic all became one Soo Line RR. Solid "Candy Apple" Red with white lettering was adopted in 1989. With any of these paint scheme changes, all the road's equipment wasn't repainted overnight, and often older schemes persisted for quite some time.
The CP had long owned a controlling interest in the Soo Line, and finally acquired full ownership in early 1990. The Soo disappeared as an independent railroad about 1992, but its name and older paint schemes linger on.