This is interesting as I have run into this problem with clock rate in reverse.
I was using 48. and had to change to 44.1 because of my Yamaha 01v.
So I have a dozen or so projects that open as 48 which makes a loud click as the audio engine shifts gears. They too are all MIDI and I thought I'll just change the clock rate, but even though it shows 48 in the Transport GUI, when I go to audio preferences it still shows as my default of 44.1. I see nowhere that you could change the clock rate other than that little box. Mix Control doesn't seem to have anything as well. So what Tom is saying doesn't really work.
I think the clock rate is embedded in the CWP file. So all I am doing is saving as a midi file and re opening fresh. Pain in the butt as then you have to re add all your soft synths etc. I might make a template and just drag and drop the midi tracks from one to the other. Only one song has a tempo map thank goodness.