Metrolink has boatloads of old Bombardier cars sitting in storage. Caltrain badly needed additional capacity but, with electrification on the way, didn't want to shell out for or wait on new cars. So, Caltrain picked-up some of those spare cars from Metrolink "on the cheap."
Some were in good enough condition to be put into service fairly immediately, but most needed some level of overhaul. As I understand, Caltrain took the easy path and turned most into bike cars, replacing old seats with bike racks.
I don't expect that Caltrain will be sinking any money into repainting cars that won't be needed in five years, unless it is truly necessary.