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I agree with you that first he asked about Jordan's friendship with Clinton, and then he asked why Jordan did not write about that friendship. I think you're misinterpreting Jordan's answer to the latter question. Here is an excerpt from the transcript on the Booknotes web site:

LAMB: How much do you see Bill Clinton today?

Mr. JORDAN: Oh, a good bit. We're either on the phone or we're having lunch at--at the Sugar Hill Restaurant or we're having supper or a drink at his house or mine, or we're on the golf course. So, we st--we'll--we will always be friends.

LAMB: How did you get to be close friends?

Mr. JORDAN: It evolved. I was in Atlanta or I was in New York. He was in Little Rock. We always stayed in touch, always stayed in touch with--with Senator Clinton, and we were just friends, interested in the same issues, interested in the same region, and that common interest kept us bound together, and we still are.

LAMB: How important do you think it was to his image in the black community that people saw you playing golf with him?

Mr. JORDAN: Oh, I think it was a reenforcement of--of his friendship with me, of his attachment to and understanding of the needs and aspirations of black people.

LAMB: Did you ever talk about the value of that when--all those clips over the years?

Mr. JORDAN: He and I? No, not really. We just did or things as buddies and friends.

LAMB: Why did you choose not to write about your friendship with him in the book?

Mr. JORDAN: Well, simply because this book covers my civil rights time. Another reason is that to some extent my--my life in the public view was defined by the Clinton presidency, and it was very important to me for people to understand that I--that the most exciting time in my life was before Clinton was president. It was the civil rights movement. It was the Voter Education Project, the Urban League, the College Fund, working for Hollowell, organizing for the NAACP. That's a part of my life and a part of my time that I have had to--time to reflect and think about, and so I wrote about it.

The full transcript can be found here.

His true motive may have been to preserve his own reputation, as you suggest. But he didn't say it in this interview.