How I understand it...
WARNING: The following is not completelly official but I think it makes a lot of sense and is not contradictory to anything I'm aware of.
BigFace was to Abe what John the Baptist was to Jesus... sort of. BigFace is the spiritual leader of all the native tribes of mudokons and was preparing them for the future. He knows all sorts of stuff about oddworld's past and prophecy. He knew that a savior was coming and sure enough, he stumbled upon Abe. To make sure Abe was ready, he had him travel through the treacherous Scrabanian and Paramonian Temples as a sort of "coming of age" ritual. After passing the tests Abe was granted the power of the Shrykull by BigFace himself.
Although BigFace was given the ability to choose and bestow the power of the Shrykull to a certain mudokon, that does not mean he can do it again or that he can use it himself. His purpose in life (and likely any BigFaces before him) was to find the mudokon savior. He fulfilled his role, but is still working to train the native mudokons.
He wasn't in AE because he didn't need to be. But he is still working hard as the spiritual leader of all the free mudokons.
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