As long as you always do that, you should be OK. The difficulty, being human, is that we have a tendancy to forget to power-off one before powering-up the other. So, expect some surprises (usally a source hang-up or unexpected settings) when that happens. Nothing that a reset won't fix until the next time.
Also remember to check how long you can go on each projector without power before you lose your settings.
Finally, I had forgotten to mention this before (sorry) but you may not need to ever power-off the 3D projector. It's only the 2D projector that will get in the way. So, leave the 3D on. When you want to watch 3D movies, power-off the 2D projector. Hopefully all of your sources will resync to the 3D EDID and you'll be OK. If you're watching 2D, then you don't care if the 3D projector is still on.