Like I said, the Dark timeline is a figment of Abed's subconscious and this was why when "Evil Abed" was born Abed suddenly "sensed" something. It wasn't just some joke, it was him having an inkling of this potentially dangerous new personality being formed in his subconscious.
And since the Evil Timeline was caused by the removal of Troy, when Abed is having issues with Troy he hallucinates Evil Abed.