You will of course run into problems if you fail an emission test.
However, only 9 of the 100 NC counties do tailpipe emission testing (WAKE, FORSYTH, GUILFORD, DURHAM, GASTON, CABARRUS, MECKLENBURG, ORANGE and UNION).
In addition, diesel vehicles, RVs AND
motorcycles are exempt from testing in any case.
So you can determined for yourself what the odds are of running into any problems.
I'd recommend changing the tailpipes and not messing with the emission system... But hey, I don't understand all that technical stuff anyway...