Locally in my area, you are allowed to upgrade a system, but you may not reduce its design capacity in any way. Sure, you could cut the lines and cap them, and maybe never have a problem, but if you sell the property, or if you have any work done on the system that requires a permit, and they dont find there in the ground what the original permit says is there, they could make you replace the system. As fast as codes change around here, if they make you replace it in ten years, you may end up with 12 or 14 lines instead of 10, or even an alternate system which could cost upwards of $20-$30 grand. I would call the health dept, and do whatever they tell you to do, because even if you sell the property, you may still be liable for what is suppose to be there.