How do we protect our margin when a customer keeps changing the order?

Put a change clause in every quote. It should say that changes are priced and that production waits for approval.

Price from real figures: material, labour, machine time and lost output. Include the cost of delay to other orders.

Keep a running total of change value per order. When it nears a set share of the order, speak to the customer.

Daily tracking makes this possible, because you see the change the day it arrives.