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The answer to your question can get pretty complicated relative to tax laws and business structure, but the most simply answer is, yes, the owner can charge one of his stores a fee.
As a matter of fact, this is a pretty common practice. You can assume that each location is either a sub-corporation of a larger corporation, or that they are separate LLCs. When the fees such as this are charged by one to another, the entity that pays the fee can often time charge that expense off as a business expense. Since they are separate corporate structures with separate tax ID numbers, they are also separate tax structures.
This is pretty common in many businesses wherein a sole owner or ownership group has multiple locations...like car dealers and even farms.
Let me know if you have any additional questions or comments.
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Best wishes going forward!