I believe you could have uniquely defined end notes in each document file (one per chapter), but not in a combined set of endnotes (using the Book feature).
End notes for, well, end notes and footnotes for chapter notes is the most likely path, although getting to your specific end needs will take some effort. (Footnotes are not any more limited in length than end notes; the only real difference is how they are organized and managed within the doc.)
There might be a plug-in for advanced academic work out there that can juggle notes in something like this manner. (No, I don't know of one.) The only solution that comes to mind is to manage one set of notes manually. Use end notes for the chapter notes, and manually manage/insert the overall book notes, or vice versa. Messy, I know.
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