Did you ever end up sorting it out? I have just encountered the EXACT same issue coming from an iPhone and using Smart switch, this is SO damn annoying. It always gets stuck on 50% and when I delete the ridiculously old messages it just automatically re-syncs them, I don't even know how or where is re-syncs them from!!!
I cannot for the life of me figure out how to permanently delete this old messages and stop it from re-syncing them!