Leanpub has a number of writing modes. If you are writing in plain text, in Markua, then you can we have dedicated support for doing endnotes.

Currently they only go at the end of each chapter, not at the end of the book.
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Here's how they work: https://leanpub.com/markua/read#leanpub-auto-endnotes

Short version:

This has an endnote[^^thenote].
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[^^thenote]: This is the endnote content.
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To put your book in Markua mode, go to https://leanpub.com/markuainbrowserdebugging/edit_manuscript_format
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To learn what doesn't work yet in Markua, go to: https://leanpub.com/markua/read#leanpub-auto-todo-in-leanpub