What personally happened to me:
I currently am the leader of the guild AF1, a retired Facebook guild fort guild. I also had my non VIP account as the leader of my private guild. I transferred the stats of my non VIP account to my VIP account and (unintentionally) transferred the leadership of my private guild to my main account, which made my main account become the leader of two guilds. Being the leader of two different guilds on a single account removed leadership privileges (such as giving powers, adding allies, etc.) from me in AF1. I decided to disband my private guild, hoping that it would give me leadership powers back in AF1. When I disbanded the other guild I was the leader of, it deleted AF1 instead.
I had to have a friend recreate it, since I did not have the 2,000 gralats. If I had taken the time to farm it, someone else might have noticed that AF1 was gone, and created it themselves, thus giving them a guild which has 1000+ guild fort hours.
tl;dr When a player transfers the stats of a non VIP account to a VIP account, it should not transfer the leadership of any guild to their main account.