Originally Posted by James Cupp
... if I was sure that swapping the upper has little or no effect on accuracy of the unit.
Swapping uppers or more specific to your question, taking it off, putting it on, taking it off, putting it on, taking it off, putting it on...will have no change in the uppers ability to perform as it always does.
It's not bad to have 2, because you can set them up for different purposes. Like, maybe you want your hog gun to be a shorter carbine style, so you could run a collapsable stock with a more factory trigger, and perhaps you want your big game hunting rifle to be more of a precision, with an after market trigger and rifle length stock.
I myself, like everything to be the exact same. I have 1 AR15 lower, and I have 1 AR10 lower...and even those are set up to feel the exact same (except for a little weight difference) Same grip, same stock and same LOP.
For me, it's comes down to muscle memory.
For the accuracy though...fear not. You'll be fine.