Why? Having a Pokedex doesn't make you a protector of anything, nor does not having a Pokedex suddenly mean you're exempt from this stuff. Heck, it's mentioned that Pokedex holders just coincidentally happen to get involved in these massive conflicts all the time. Also, there's no rule stating a Pokedex holder can't leave their region. They do it all the time.
Second, there are a variety of other characters that could protect the region, like Gym Leaders or the Elite Four. It's not just the holders.
And lastly, why should they give up their Pokedexes for any reason? Even if the new kids take over, it's not LGPE uses the same model as FRLG, right?
Sun and Moon are two months after XY's ending (so five after Team Flare's defeat overall). And the scene where Sycamore talks to Green and Blaine about sending Sina and Dexio to Alola happened before the three month time-skip, so he could be anywhere.