Yes, limits are adjustable, but only to some point. Problem is, with a really old collection I just don't know how many files are there. I probably am, as 100 folders is really not that much. So if the limit is hit, I will never know. Some message about this comes to my mind, but I am not sure it will be really useful.
Depth limit -- understood. Personally I'd prefer 99 to current 9..

About the _Rejected in subfolders mode. So, what is the recommended process, 2-pass? First mark pariahs somehow and then walk across the folders and move them for real?