Yes and no... you will bypass the subwoofer effect of the ANC, which was not noticeable to me. I did not think initially it was doing anything. I unplugged it and did not notice any noise like I did with my previous RAM with the Alpine system. I unplugged that sub and noticed a significant increase in exhaust noise, but not so with my eTorque. My suggestion would be to unplug it and make sure you don't notice any adverse effects. I know it works in the ANC, because when I first used the sub speaker leads to feed the line converter, I noticed a droning noise in the sub when I would let off the gas pedal, which told me there is something the ANC is trying to eliminate. My wife nor I could ever figure it out, so I knew if I went with the PAC, it would resolve the issue. My other ANC speakers, front door and rear door are doing what they should. So... not knowing if your truck will react the same as mine, it's hard to say for sure, hence my suggestion to unplug the sub first to make sure it's not noticeable like it's not in my truck. My wife as cat ears, she can hear stuff I can't... unbelievable how good she hears.
I let my wife listen to the noise last night by using the ANC bypass adapter, and we both could hear the exhaust noise, more specifically when giving it a little gas going up a hill. It's not bad, but it's noticeable... and the ANC gets rid of it using the front and rear door speakers when I remove the bypass adapter. I had installed a full aftermarket system in this truck (info in this thread), then she finally decided she needed a new car (over 100K miles on her old car), so I took my aftermarket system, less the JL sub and amp, and I am currently installing it in her car with the JL sub and amp that came out of her old car.. I wanted her to hear what the ANC is doing to help me determine if it's worth sacrificing the ANC to install a full aftermarket system again after I finish up her car. I'm still on the fence, as I really like how quiet the truck is with the ANC.
I've came up with another idea I think will work to allow me to have the aftermarket system and retain the ANC. I have already learned that I can take the bypass adapter and move the pins from the radio feed positions to the mic feed positions. This will then block the radio from feeding the amp and instead allow the mics to feed the amp, basically reversing the adapters original design. The problem is I need to replace the door speakers, so that eliminates the ANC in the front, and you need all four speakers, front door and rear door for it to work properly. So.... I am going to find a fiberglass guy and have him mold a speaker housing in the lower portion of the door where the dual cup holder is on the left side and where it would go on the right. There is enough room there to get a 6" speaker at an angle firing up, and make it look almost factory. I will use this speaker as the factory door speaker, which will continue to process the ANC along with the rear doors, which I don't use in the aftermarket system (I use the rear headliner speakers for rear fill). So the "new" front door speakers and rear door speakers will continue to process the ANC, but will not get any signal from the radio with the reverse pinned adapter. Bingo! The best of both worlds. Now I just need to find that fiberglass guy who may have to borrow my door panels for a couple of days.