Huge ones actually. Any progress you've made in any of the quests would be lost. Any items you've acquired would be lost. It's something you should only do prior to activating them on a particular character.
I can't guarantee you won't get screwed up results anyway because none of them are merge-safe as far as formID collisions.
Thanx mucho, Arthmoor, for the update on Faregyl, Urasek, and (although I don't think you announced it, I found it anyway) the updated patch for Shezrie's Lakewood Village and Aspen Woods. :thumbsup: