Sat, long time no see. Wish I had some great advice to welcome you back with, but if you mean that the sub works normally when Audyssey is off, but has no output whatever with it on, that's a puzzlement. Audyssey can adjust the relative volume levels of the speakers and sub within certain limits, but has no capacity to turn one entirely off. I'm not familiar with your car setup.
Are you sure that it isn't just a lower(better balanced)sub level which makes it "disappear" compared to previous boominess? Some users have gone as far as to claim "It stole all my bass!".