If Silas enters R'lyeh, he fails his personal story and becomes a Deep One. So... where is the Deep One placed? R'lyeh? The last place in Arkham that Silas was in before entering R'lyeh? What happens if he's in Lost Carcosa and he has an encounter that sends him to R'lyeh? Is the Deep One placed on the Arkham location with the open gate leading to Lost Carcosa?
I suppose there's no reason why a Deep One couldn't be placed in R'lyeh. You'd fight it during your Movement Phase, like normal.
Sorry if this has already been answered. I did forum search and I saw that the question had been asked once, but it didn't receive an answer.
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