The problem I tried to describe is where in the middle of a run of pages with footnotes, with one text frame per page linked fore and aft, IDCS4 suddenly decides to leave an entire frame blank and flow the text into the next page and frame.
So far as I recall, this occurs in files born in IDCS4, with text from MS Word files prepared in a separate dummy ID file to remove all MS Word styles and to apply the correct fonts. And sometimes it seems to happen between the time I saved and closed the file and then opened it again, i.e., without my making any changes at all. It is not a matter of keeps options (I generally define the auto footnote paragraph without keeps — I usually apply “keep last two lines together” by hand only as needed). It is as if, in re-flowing the text, ID gets confused, forgets about the whole frame, and goes on to the next page/frame.
When this happens, I don't think I've ever tried David Blatner's trick for forcing a text reflow<https://creativepro.com/force-text-reflow-when-indesign-forgets-to-flow-the-text.php>, “Recompose All Stories” (shortcut Command-Option-/ (slash) or Ctrl-Alt-slash). Perhaps my habit of lengthening the frame is equivalent to his double-clicking the text frame, though sometimes I must leave the frame a shade longer to maintain page-breaks.
As for catching frames that are not of a specific length, I suspect that's scriptable.
David