I'm using ID version 16.21 and have just had a similar dropped footnotes issue: in the middle of the book, suddenly, 10 pages without footnotes, and then after that, footnotes again. The author has counted 22 footnotes dropped. I'm on a very new, high-specced PC running Windows 10, so I think it can't be a hardware issue (I gather some users on Mac had a similar issue). And the job was (I thought) near completion, so starting again and converting the Word docx to doc (as has been tried by some others who had this issue before me) is not an option I am keen to be forced to try, because I have also done a significant amount of work to convert tables and such-like.
If this is relevant, the Word docx was edited by a professional with a lot of technical editing experience, and experience using Word, so I think it is not very likely that it arose from clumsy use of Word, as is so often the case.
Thanks in advance for any solution you may be able to offer.