Hello Jorge,
This is not recommended. While, two instances of Matlab, each running Brainstorm, and each Brainstorm using a different Protocol sounds kind of safe, it could lead to unexpected behaviour, and files / database corruption. This is because the current database system was not design to handle concurrent access. We are currently in our way to update to SQLite-based database system that will address this issue.
Moreover, computation times may not be greatly improved as many processes already use multiple cores.
A more extended answer here:
Best,
Raymundo