You'd have to check your insurance to see if voltage surge damage is covered; I would doubt it, simple because the nebulous nature of that claim would expose insurance companies to fraud. (I'm not saying you are acting fraudulently; just that surge coverage would make it easy for fraudsters!)

What you should do is install surge protection -- especially now that there is a pool rated model with insurance(!):
Intermatic PS3000 Pool Surge Protector
However PoolSean (Auto Pilot service manager) has told me that the Auto Pilot units contain surge protection, which may now need replacing on yours. I'm going to ask him to check on this.