The terms of Gap policies can vary however if your primary insurance company denies the claim and thus does not find this to be a covered loss and pay out the actual cash value (ACV) for the vehicle then normally your gap insurer would not pay out either.

Gap insurance fills in the difference between what is owed on your loan after the ACV is paid for a covered loss. If your insurance company has turned down your claim for your car that was struck by lightning then ACV is not paid out and thus the "gap" is not there, just the full amount of your loan balance which GAP usually does not cover.

Read through your gap insurance policy and discuss this issue with your gap insurer to find out for certain though what will happen in your specific situation.