Once or thrice, this doesn't matter. After a few times through the action though, this will 'push' the bullet back into the case enough that it's compressing the powder more than it should. At that point, you have added a +P to whatever you started out with. Do it enough, and it causes undue stress on your chamber and barrel, and eventually could lead to a ruptured chamber.
There are a few ways to deal with this problem.
Some will just leave the top round in their chamber at the range, and shoot it with their practice stuff, and top of the mag with a new HP when they get home. Some will throw it in with the practice stuff after a few chamberings.
Personally, I paid too much for the carry stuff to not get the most out of it, so every two chamberings, I actually unload the magazine, and take the top round and put it on the bottom. I mark the 'first' round of every mag with a sharpie, and when it comes back up to the top, I move that mag to the back of my spares. When I do this with all three mags, I shoot them all at once.
It's a pain, and probably overkill... but I'm cheap :)