As Nelson saidsaid, just sending your dwellers out of the vault won't let you destroy all your rooms to rebuild.
What you can do, however, is rebuild step-by-step, or build some temporary accommodation out of the way somewhere (probably in a very deep level) then destroy all the other rooms and rebuild. I've done this a couple of times. If you're planning on moving your lift shafts around it can be a faff, but it's eminently possible.