I have replaced a 5-way rotary with a 3-way toggle on my 97 CE 24. It requires making the hole the switch shaft goes through a tiny bit larger. I think I just carefully sanded the edges of the hole until the toggle shaft fit through. I have since replaced the toggle with a rotary and it works fine, so the change wasn't "irreversible" in that sense.
I have also replaced a 3-way toggle with a 6-way toggle on a different guitar. No need to adjust the size of the hole for that swap.
So, my guess is you'll have to make the hole a little bigger for the 6-way after you remove the rotary, but I can't say that with 100% certainty. As far as the 6-way toggle working, I just followed the soldering instructions that came with the switch and it works properly. The switch I have gets all 5 of the rotary combinations plus both humbuckers together.