With the last patch, I feel like there’s been a regression with the Silent Assassin in Freelancer mode. It works like Hitman 2016: if a target sees us committing an illegal act, it permanently breaks the Silent Assassin. I’m not 100% sure if this started with this patch. See for yourself:
As I understand it, in Freelancer, the only real Silent Assassin is the Prestige Objective, and once it is lost for whatever reason, it is indeed irrevocably lost.