The last ebook I edited which had multiple footnotes in one file, I ending up splitting the file into 5 chunks with ~50 footnotes in each to reduce the size of the individual files without giving each footnote it's individual file.
Since I did this as a manual process, I opened the original file, divided the line count by 5, went to the 80% mark, pasted a Sigil split marker ( <hr class="sigilChapterBreak" /> ), went to 60%, 40% and 20% and repeated the paste. I then did hit f6 to do a split on markers and it was done. The only issue I ran into was that while this looked good with pop-up footnotes, for non-pop-up footnotes, I ended up copying 6 or 7 footnotes so they were 1-to-1 and not the original many-to-1.
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