Yes Caltrain (actually the Peninsula Corridor Joint Powers Board that owns the track) has a clause in their contract from when they bought the line from Union P

Yes Caltrain (actually the Peninsula Corridor Joint Powers Board that owns the track) has a clause in their contract from when they bought the line from Union Pacific that states they can start freight abandonment proceedings if they make a significant change to the line. It's generally believed that was put in there in case they wanted to convert the line to BART, but in theory it could be brought into play for a Caltrain electrification or the HSR project. Caltrain has so far, however, refused to go down that route. Apparently the one freight train per day is too much to lose.