according to the autopilot info, if you shock with an autopilot, you should use a non chlorine shock. i would guess it might screw up the cell if chlorine based or there's something in a regular chlorine shock chemical versus the chlorine the an swg produces which is believe is a less complex chlorine than "bottled". at the least i would turn off my swg unit when shocking with chlorine bleach for example, but to be safe, i've emailed poolsean with autopilot to ask him to clarify and i'm sure he'll let me know by tomorrow or post the answer here himself. i only have needed to shock at start of season when i have my manifold swapped out for the tube. i remember once last year when i didn't pay attention and my pool went green in summer under my cover, but i'm sure it was before i got the autopilot..i don't recall having any concerns like this