Hey gblotter,
Yes, our Stake had our Troops, Crews and Teams all registered individually, luckily I didn't have to deal with the recharter headache but from what I heard it was a real pain.
We had the same mass migration, my understanding is that the boys were co-registered sometime in August or early September in the Crew and in the Troop, they weren't sure at that time what they did with the leaders records but our advancement person was going to manual register us as ASMs during recharter to avoid any possible issues.
Your experience with how the Crews and Teams ran is exact