[drdisque]

Your mechanic is clearly not any sort of exhaust specialist and doesn't really understand modern emissions systems.

You can replace your mufflers with any other mufflers you want to, including flowmasters. You could even completely remove them and your computer would be none the wiser.

However, yes the car would throw a code if you removed the catalytic converters and it would negatively affect fuel economy. However, they make little things called MIL eliminators that are plugged in in place of the O2 sensors that make the code go away and the car operate normally.

Also, note that it is illegal for a shop to remove the catalytic converters on a street-driven vehicle, so if you want to remove them you'll have to do it yourself or find a shadetree mechanic to do it.