Wholesale and Retail

Just looking for a little insight.  I have a client that has a wholesale store and retail that he and has  combined the sales part of the retail side along with the wholesale, creating one P & L.    He sells jewelry and has inventory.   He invoices the retail side to pull the inventory for the product sold through the retail store. He does not mark up the invoices.  The markup is done through the retails sales to customers.   So, my confusion is that the jewelry sales to customers is entered in,  but also when he creates the invoices  he invoices to pull out of inventory is also entered as income.  To me the income is done twice.   Through the sales to the customers and what the whole sale side invoices the retail side.  Am i seeing this correctly?  Is there a better way to do this?