I don't think the challenges should affect whether you can get silent assassin rating or not - more challenges completed means your end score will be higher - MUCH higher if you get silent assassin, but I don't think the 2 are necessarily linked.
just about to test that out as I think I have figured out the silent suit only route for Terminus Hotel. I've already completed the second part silently but didn't get a silent assassin rating as I knocked an electrician out in the first part to get his outfit.
Yeah, I completed the level without being spotted and even managed to do it suit only, without knocking out anyone at all and still only managed 'professional' or 'shadow'. Some gamers have suggested there's no Silent Assassin rating unless there is a target to be assassinated. Makes sense but I wish it could be explained. The handbook for the game is rubbish, especially compared to previous games, although the game itself is outstanding. Peace - MWK