I picked up a carbon HT 29er this season to compliment my FS 29er. I used the FS 29er for two solid years of XC and endurance races. Having done that, I definitely saw the need for a HT and something lighter/stiffer/racier. I love that this year I will have a "horses for courses" option. I too can swap wheels back and forth if I need to which is nice. Both bikes are running the same tire setup as of now although I don't see that as staying the case.
As far as bike feel, going back and forth, I don't really see it becoming an issue. If you spend enough time riding your bikes, your body will develop a muscle memory of how that bike fits. Within 10-20 minutes on it each time and you will feel right at home. I notice the biggest difference after I go from riding my road bike for hours on end, to the FS 29er. I feel like I'm sitting straight up and about to fall over the back of the bike, a few minutes later and I'm fine.
Go for it.