With Harmony Hub, the Hub holds the status, not the remote -- therefore everything is automatically always "in sync". The iPhone and Android apps are automatically notified by the Hub whenever a new activity is started (either via the remote or through the native iPhone/Android app running on another device or through the HarmonyHubControl app) and all devices update their displays accordingly.
I suspect the same goes for the Harmony Ultimate remote since it also uses a Hub, but I do not have one to confirm.
I find that using the iPad mini to control both scenes on the Vera and Harmony activities is quite convenient -- especially if you map desktop icons to the URL's of your Vera scenes.
The idea is that once the Vera can control the Harmony Hub it will be able to access the last few components of an entertainment system (including the PS3!) so those can be scripted into Vera scenes. There are, of course, plenty of other ethernet-IR bridges, but the Harmony seems to provide a very polished experience.