The email exchange, which took place last July, involved the show's executive producer Henry Louis Gates Jr and Sony Pictures co-chair Michael Lynton.
In the leaked messages, Gates asked Lynton how he should handle Affleck's request, in which the 'Gone Girl' star asked that the docu-series withhold the information about his slave-owning ancestor.
"Here's my dilemma. Confidentially, for the first time, one of our guests has asked us to edit out something about one of his ancestors--the fact that he owned slaves. We've never had anyone ever try to censor or edit what we found. He's a megastar. What do we do?," Gates wrote.
Gates replied, "It would embarrass him and compromise our integrity. I think he is getting very bad advice. Once we open the door to censorship, we lose control of the brand."
Affleck's name is not mentioned in the email exchange but the actor is referred as "Batman" and "a megstar."
The episode on Affleck focused on the actor's mom, who was a "freedom rider" in the 1960s but there was no mention about the ancestor who owned slaves.
PBS posted a statement on its website saying: "It is clear from the exchange how seriously Professor Gates takes editorial integrity.
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