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Yes, the lack of multi-level TOC support on the Kobo can be quite an irritation. The version of "On the Origin of Species" in the 100 pre-loaded books for the Kobo has 4 top-level entries so that the book is essentially one long "chapter" of over 500 pages.
I'm not holding my breath in anticipation of a firmware update for the Kobo that fixes the problem (nor for an update that supports soft-hyphens, another bugbear for me).
I check, and edit, any epub to be side-loaded onto the Kobo. For the TOC, that usually involves making a single top-level entry for each chapter; for the stylesheet(s), my preferred layout is indented paragraphs with no spacing between paragraphs, and with no preset font (serif or not); for the text, the format for anything in verse form has to be altered for indentation and wrap-around.
In your case, I would probably split each of the large epub files into a number of smaller ones. If 7 pages of TOC entries with 1 entry per chapter were the maxiumum desired, that would mean around 17 epubs for an epub with 115 TOC pages. For the omnibus, I would split it into separate volumes and edit the TOC in each case to give a single TOC entry per chapter.
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