Baker testified on March 25, 1964. The amended affidavit (probably prepared by FBI agent Richard Burnett) that's in question was signed on September 23, 1964. So there was nothing to clarify at the time of his testimony.
My understanding was that the WC was closing up shop and rushing through affidavits to meet the schedule.
Jean Davison made this point: "Baker's affidavit of Sept 23, 1964 and a similar one from Truly were dated only one day before the Warren Report was officially released, and both their statements were, unlike all the other FBI documents I'm aware of, *handwritten*. IOW, they were prepared in a big hurry. Their statements are footnoted to a WR paragraph on the "rumor" that there was someone else in the lunchroom when Baker confronted Oswald. (Neither Baker or Truly had been specifically asked this in their testimony. Their 9/64 affidavits supplied the explicit answer: no one else was in the lunchroom.) I surmise that someone at the WC realized at the last minute that they needed a "cite" for this statement.""
David Von Pein has more details on it here: https://jfk-archives.blogspot.com/2010/07/oswald-baker-truly-and-coca-cola.html
Thanks again, Steve. I now remember reading - possibly in one of the books by one of the WC attorneys - about the circumstances under which those affidavits were prepared. Still, only in the JFKA, where nothing goes smoothly, would the "holding a coke" statement "just happen" to find its way into a draft affidavit and create havoc.
Here is an old thread (2010) from the McAdams forum on Google in which Jean Davison participates and speculates the handwritten affidavits were prepared by an FBI agent who prepared them in advance and simply included the "established myth" about the coke. DVP suggests basically the same thing. Pretty weak, it seems to me, and in any event how this damning statement appeared in the draft affidavit should have been firmly nailed down.
https://groups.google.com/g/alt.assassination.jfk/c/_TSEJPDFU4c/m/LWDpqCFXF94JIt looks like DVP's site may preserve the same thread, but I find it impossible to wade through these endless "and then he said" discussions. I just happened to stumble immediately on Jean's contribution.
Dulles (of all people) somehow knew to ask Truly at the WC specifically whether Oswald was holding "a coke." When Truly said no, Dulles asked whether Oswald was holding any drink. I suppose Dulles could have been informed enough about Oswald's alibi to know he had claimed to have bought a coke.