I solved my VC problem. This is covered somewhat in the help regarding packages and sequence diagrams. Sparx would have you keep the actors under each package and then if you were to resue the actor, instantiate it. The challenge is that this becomes very messy and hard to find actors in very large models.
You would have to open every package to see if an actor that you want has been used before.
A better practice is to keep a separate package for actors. This way you can develop a canonical set of actors with organizational agreement on the roles, descriptions, etc. Every works from the same set of actors and if a gap is noticed in the actor set, the team can have a discussion around creating a new actor. This is just good governance.
Anyway the way to fix my problem was that we had:
root -
- package1
- package2
- package3
so if actors were in package 1 and used in package 2, if notes were attached they were not exported in version control.
The ACTUAL fix

is to have a parent package, (no need to instantiate) so the project structure should be:
root -
- parent package
-package1
-package2
-package3
when this is put under version control notes attached to sequence diagram messages will now export correctly.