To answer the OP's question: Pretty much any variation from factory original will hurt resale value. This is especially true if it is a "bubba job." But, you won't know how much money you will lose until you sell it.
The real question is: Should you cut it down? The best option is to buy an after-market stock, and make any modifications to it. This allows you to make the gun fit you, while preserving the factory stock in original form.
