I have a book with a number of footnotes, with the number restarting on each page. Under various circumstances, including the text having the note moving to a new page, the footnote is not renumbered. Using F9 and Tools > Update All has no effect.
My work around is to change from numbers to Roman numerals and back. Also, if I change the Counting to Per document and back to Per page, everything updates.
I tried reproducing it in a small document and was unsuccessful. The document where the problem occurs is 180 pages long, single spaced. I have also noticed that automatic spell checking stops working if too many errors accumulate, although that is easy to fix by mass correcting problems.
I suspect that an internal timer is stopping the updating process, due to the size of the document and the number of footnotes; this would prevent the application from becoming sluggish.