I think you're talking about 2 different issues here. First of all, your followers disappearing in the air does NOT mean you lost follow. Please get a mod (like multiboxer v2) that shows your slaves follow status and you'll notice that most of the time your slaves disappear they're still following you. This is because you're moving too fast for the game to keep up with the drawing, so your followers will "disappear" until the game figures out where they are again at which point they'll reappear. On your minimap it will look like they've fallen way behind, but if you keep flying eventually they'll "snap" back to you again.

I can personally fly from one side of northrend to the other and the only place I will "actually" lose follow is crossing through phased zones, which is mainly just icecrown and a couple areas of storm peak.

So the first thing you have to determine is whether you're actually losing follow or whether you just think you're losing follow, I'd be willing to bet most of the time its #2.