"Well lucky me!
I discovered that the bass line IS MIDI!"
OK well I opened the Help file and learned that you move the note by clicking the Middle of the note bar...
Now the problem I have is when I re-generate the song, the notes go right back to what they were originally.

How do I FREEZE just the notes I changed?
Funkycornwall has given you the best suggestion in my opinion.
I think what you've run into is a RealTrack with a Real Chart. If that is indeed the case, anytime you re-generate the track, the RealTrack will regenerate and so will will the Real Chart. It will change to conform to the RealTrack.
To have your bass play the Real Chart, you will have to change to a midi bass instrument. That's not a bad thing because you can then notate the bass to play whatever notes you choose and desire.