I heard that a part of the Shri Sai Satcharita might be missing or was not published as originally intended. Is this true?

Yes, there is evidence to suggest a deviation from the author's original plan for the book's conclusion. In Chapter 0, it is noted that Annasaheb had written in the first chapter that he would provide a summary (Simhavalokan) and a conclusion (Avataranika) in the 52nd chapter. However, the published version of chapter 52 lacks these elements. The prevailing theory, also mentioned in Chapter 0, is that the slips of paper on which Annasaheb had written the verses for this summary and conclusion were likely lost, as it was his habit to write on such slips.