There are a few ways to copy things in BIAB. You haven't told us which one you used.
From the sounds of things, you've employed a process that also copied and pasted part markers. That would cause BIAB to re-generate the next time the song started.
As I mentioned in an earlier post, the Melody track and the Soloist track don't regenerate (unless you have a Realtrack or MIDI Supertrack loaded on them).
With this in mind, and if you have a recent version of BIAB...
I encourage you to follow the sequence of numbers on the image below and...
1. copy your MIDI bass track to the Melody
2. work on the notation on the Melody track
3. When you get it how you want, move the track back to the Bass track.
BEFORE DOING THE ABOVE, though.... make sure that you save a backup copy of your song. Then, if something goes wrong, you can get back to where you were. Also save a backup with another name before you send the bass back to the Bass track.
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