[Geoff Bacon]

I find that when I replace a song using the companion, I have to then modify it to remove my annotations about what I needed to change). Should be the same if you use the MSP menus.

So, duplicate the album version and annotations using long press and "copy song" as indicated above

Then replace one of the songs with the "live" version. This will then have the live version display with the original annotations.
Adjust as necessary. 

Geoff