Sounds like you are talking of the o2 sensors. They should be able to be installed in the new pipes. If you do disconnect them you will get codes and the eng lite on. The BR pipes have bungs for these sensors and if not using a fuel control that doesn't use the o2's like a PCIII then I wold install them.
yes i saw that in my manual. it is an option. you wont use it any longer when you change pipes but i donot think it has any electronics that would cause an error code but i will look, it is called active exhaust and it has no electronics