I don't think Intel System Studio for Microcontrollers supports updating QMSI version, but here is a workaround you might want to try:
1. Create a new project in Intel System Studio for Microcontrollers. This will copy the QMSI version supplied with Intel System Studio for Microcontrollers to the bsp subdirectory in the new project directory (workspace/<project_name>/bsp).
2. Get the new QMSI version - download a ZIP file from the GitHub and unzip it, or do a "git clone".
3. Replace the content of the bsp directory with the new version.
4. Continue with the project development.
It is possible that new QMSI names the output binaries differently, or puts them in some another directory. If so, it is necessary to change the locations of the files in Run/Debug Configuration (in Run menu).