Equipment generally does run, however once the firmware starts updating, modules will lose connection with the communication controller and then proceed to fallback settings while the update happens. It is a good idea to review fallback settings before updating to ensure that during the update the desired operation is in effect. In some cases, depending on the update, some modules may be disabled after they get updated (like after significant feature updates that cause settings changes) until the system completes the update and boots up so that all settings get re-pushed down to the firmware.