I'm not sure that the Soo line runs as an independent subsidiary of CP... The last new locos acquired by Soo were the SD60Ms in 1989, and I believe the last repaints in Soo colours were done in 1993... after that, I think everything was getting the Dual Flags scheme.
Anything delivered after the merger would have been painted for CP. I don't think CP assigns units to its subsidiaries, or identifies where they came from (as NS did by having the former home-road initials under the road number).
After 1997, CP reorganized itself as Canadian Pacific Railway, and I believe that meant that all the subsidiary roads (Soo, D&H, StL&H) got sucked back into the big corporate whole.