I'm in the same boat - been wrestling with this for hours today. I've been experimenting with ways to "trick" Bittorrent Sync into thinking that it's already updated - like, starting with a blank folder, moving the files over and then hoping it re-indexes. Haven't had any luck thus far - my experience has been the same as you describe. I have a similar amount of data (hundreds of GB), so it doesn't make sense to let it delete & re-transfer. Any tips?