Another case where Transform tool can be very handy is replacing one synth/VI with another. You'd want to keep original performance but will have to re-adjust some CCs to suit the new instrument response.

AdamGrossmanLG
when i try to use the transform too it erases my CC data.. if i move the window to the right to focus on those notes, it wipes out everything i scroll through.

There is definitely something else going on there. I have never seen this behaviour. 

When this occurs, are you sure the actual CC data is being removed and that it's not just your graphics playing silly beggars with the representation of that data?