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If it's a complete number matching car-yes it would hurt. If the LT1 motor is gone it doesn't matter,the collector value has dropped too.
I'm pretty sure that you would have to make a number of cuts. As a rule, you assume that a modification will reduce the value by the cost of returning it to original. In this case, it would be more than just unbolting the add on system. It would be repairing and replacing altered and cut parts.