Sorry you're in one of those cities that charges by sales. I have a client who is in one of them. I've been lucky and always had a flat $50 license fee.
The thing about the income tax return is that if you get audited, you may have to account for all the deposits that went through your bank and that would include checks with reimbursements built in to the total.
What I do on my return is count everything as gross revenue, then subtract the reimbursed part as "returns and allowances" on the grounds that the money was "returned" to the company when you bought the Happy Meal. It's like if you're a brick and mortar business and sold 10 widgets and someone returned one, your starting point for your business license calculations would be 10 minus 1. The "return" isn't an expense, it's an un-sale.
Time to build a bigger bridge.