It sounds like the big box stores themselves are validating the Strong Towns interpretation that towns have invested far too much public infrastructure compared to the property value of the big box stores (https://www.strongtowns.org/journal/2017/11/3/big-box-stores...). Perhaps these towns could zone every big box store for subdivision and redevelopment so that the stores will have to pay taxes based on the upzoned value. As an added benefit, the stores will be encouraged to use the land more productively.
Indeed, a possible compromise is that if the property is to be taxed as an empty store with no customers, then it should be supported by the infrastructure needed for an empty store with no customers.
Maybe toll roads or an extra tax for these types of properties if they're active rather than derelict. Price them so that the companies will choose to pay tax instead.