A lot of those problems are dependent on when the mass exodus of magical critters took plsce, and a lot of the others can be filed under 'magic'. Communicating exclusively to your people is easier when you have techniques the outsiders don't. If you pulled the old time-travel cliche of giving the Romans radio, the Ostrogoths aren't going to be intercepting their communications short of stealing a radio (not possible in this case, since Muggles by definition
don't have magic) or torturing it out of some poor bugger (possible, but might not help if the magic types are in invisible cities or behind probability barriers created by weaponised good luck charms or whatever)
And if the seoaration happened far enough back, the dissenters would, in all likelihood, have long since been hunted down and messily killed. Which would tend to prevent the rise of new dissenters :-/
Coordination could be as simple as whoever made the hiding possible in the first place saying 'we're getting butchered out there, here's a refuge, here's the rules if you want in'. Moving a million+ people... again, if it happened far enough in the past, it wouldn't matter as much. Modern archaeologists might find some traces of weird, but likely nothing conclusive (nomadic societies just don't leave all that much behind). That and the world is simply a lot bigger than most people think; I mean, it's not physically larger or anything like that, but there's a hell of a lot more empty space than most people realize.
edited 14th Mar '12 12:17:14 PM by TeChameleon