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Hm, I think I would end up creating one field per product in the Customers table to represent the price override, and so for example if Customer 1 has a price override for Product A, I'll put fill in the 'Product A' field for Customer 1, and leave everything else blank
Then in the Sales table (or whichever equivalent table where you link the product sale to the customer), use lookups and formula fields to check whether there's a price override