Even if there is deconditioning, things will probably improve pretty quickly and with little effort once you're doing better. When I have had brief remissions, I had a day of mild soreness (which felt great!) and that was it - it was suddenly easy to do much more than usual. No long and difficult struggle to gain additional strength, etc etc.
I've had a similar (though milder) sustained effect since starting Yohimbe. Suddenly walking up and down the stairs is just easier. I don't do it any more frequently than before, and I didn't have to train up to it. I just got a slightly better handle on my symptoms and the changes came like I'd just flipped a switch.
So I think it's best to listen to your body, and ignore the "deconditioning" psychobabble. Deconditioning has such a minor impact and is so quickly rectified when health improves that it's not worth worrying about it. You're not giving up on your health - you're doing what's smarter for your health at this point in time.
