In this case, its always recommended to stop running applications and devices if performing maintenance on the system and running windows updates. I seen cases where it stops and halts operations needed by application, because it needed to update lower level components at the windows level of which the app may have been touching during its runtime.
Note overall, there is a note in the SR 6.0 release update for this in section 1.8:
www.dialogic.com/.../release_update.pdf
Regards,
Jeff