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its a matter of calculating the business case including the whole benefit analysis and risks, also the strategic importance of the customer. if by making those features, you will ensure customer loyalty and a longer term commitment or additional volume for example that should be evauated against the total additional cost that you would make.
There are many options: 1. Negotiate with major customer, it is always a delicate matter. 2. Share these costs between you and customer 3. Increase the sales volume to major customer and accept lower margin 4. Increase the price of basic product and offer additional services in package 5. Diversify the portfolio, accept lower margin on major customer and find new customers with bigger margin compensating that loss 6. Offer more products to major customer, increase the dependency on your products, decrease the willingness to change you as a supplier and negotiate better conditions for the future