Thanks for replying. Neither exporting as .idml nor deleting the preferences files worked.
If I go into a footnote downstream of the changed note, delete the footnote number, and choose Type > Insert special character > markers > footnote number, the correct number appears, and it behaves correctly if I change the numbering sequence between each page and section. So I have a fix, but it will take forever. We publish academic books, some of which have hundreds of footnotes.
I have never seen what you describe, and I've set scores of academic books and journals, many with several hundred footnotes, going back to before ID could "do" footnotes and they required a separate text box adjusted by hand (à la PageMaker). Maybe I misunderstood, but I wonder why you need a section on the first page: sections are an aspect of pages rather than text flow, so ID allows just one per page. Every now and again I need to change the numbering within a page, and when I do I fake one set notes so I can control the numbers.
Much more often, I need to add an un-numbered or asterisked footnote above the first note, generally the author's acknowledgments. The workaround for this is to insert a carriage return before ftnt 1 and type the note on that new line (I often use a separate paragraph style). ID doesn't care, apparently thinking my addition is part of the first note. If the first page doesn't have a ftnt for me to sneak the acknowledgments into then I do it the old-fashioned way, in a separate text box at the foot of the page -- easier than messing with sections.
Thanks for your excellent note, David. My first dtp experience was with PageMaker in the '80s, when it still belonged to Aldus, so there are features in InDesign that I recognize (like the story editor--why is that still hanging around?), but I've been in book publishing and using Quark for twenty-five years, and it's very frustrating to run into a problem in InDesign and not have a clue. I'm not used to that scenario.
I think I've figured it out. The previous publisher's typesetter, for some unknown reason, seems to have manually numbered the notes, but not the note references. So the notes reflow with the text, but don't renumber when another is inserted.
Curiouser and curiouser. Thanks again,
Actually, the story editor might been the most direct way to see that the note numbers in the notes had been altered manually because it would show the digits as ASCII text (I re-confirmed this for myself before going off on the tangent about notes ahead of the first).
Just to mention another gotcha with footnotes in ID, they don't play well with XML, as occasionally discussed down the hall on the ID Scripting forum.