Just don't flip it while the machine is powered on otherwise Alice would probably be toast.
I seriously doubt that.
Though I can't truly vouch for Alice (never owned an AGA machine) Agnus doesn't care at all if the switch is flipped 'hot' (used to do that on a 500 and a 3000). Since Alice is more-or-less just a newer rev of Agnus it shouldn't be more picky.
