Air for a minute while shaking shouldn't case a problem. The warnings on the zeovit literature are to make sure the stones are not dry while the pump is off if you are running the reactor 3 hours on, 3 hours off.
I'm using a three fishes phosban reactor for zeovit. I have a shutoff valve just before the reactor so don't need to remove the hoses when I shake it. Just turn off the valve, pick up the reactor and shake, hang it back on my tank, and turn teh valve back on. Once teh flow is turned back on any air bubbles get pumped out.
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