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No. What would It That Fled do in the same spot, whether it is part of the Syndicate or not. Why would we let a member of the Syndicate stay in a secret thief's guild. Why would It That Fled be willing to work with me while also in the process of being used by me as a particularly red pinata.
You know. Those things.
Betrayal NPCs only appear in the Rogue Harbour if they are not currently part of the Immortal Syndicate (i.e. not on your Betrayal board).