Acknowledging an existing working chassis will cause everything within the chassis and both IOM modules to restart. You will have no network or San traffic through the affected chassis during the acknowledge process. You should vmotion off all the blades operating in the chassis you want to acknowledge and then they won't be impacted.
I retract what I said earlier. Acking a chassis won't reboot the blades but they will lose connectivity for 30-60 seconds. Note that will include SAN traffic. Plan accordingly.