Reflowable ePubs and Endnotes

I think you're describing two different things: setting a style on which to break (create a new page, as for the beginning of a chapter -- recommended by Amazon) and how ID handles endnotes. I've just successfully produced an ebook that has hundreds of properly linked endnotes and that breaks on chapter head style, and also has all sorts of internal cross-references, so I know this can be done. Both Adobe Digital Editions and the Kindle Previewer honor the link between endnote position and citation position.

That said -- use Edit All Export Tags from the paragraph menu pulldown (for each file/or synchronize) to make sure how your styles are labeled and which style(s) you're breaking on. Don't duplicate the style names (that is, don't name two different ID styles as the same output style). All files in the book (including TOC) MUST include all the same styles -- whether or not they're used. This makes a more efficient ebook. Before exporting to EPUB mark the TOC with the "synchronize" marker (so that you can identify the TOC file when producing the EPUB). Don't use spaces in the output style names. Use hyphens if you must.

Endnotes: Well... the author of the book I worked on produced lots of endnotes for the print version (POD), and there were hundreds of them. However, ID's EPUB export function apparently prefers to work with footnotes... So I converted them. And in the EPUB output process, there is a switch to make them endnotes again. Go figure. There is a built-in converter between footnotes and endnotes in the ID Type menu. With 12 endnotes, there should not be a problem... My author slathered 75-100 endnotes on a single item, and ID could not convert the page to footnotes. He had to eliminate some of the endnotes. Test your endnotes/footnotes in InDesign to confirm that they are linked. You can right-click the number in each case, and you should be able to go to the correct location. If that's not working in ID, it is unlikely to be working in your EPUB. If the endnotes/footnotes were entered correctly in ID to start with, they should output appropriately connected. Should. I don't know what might have happened to make them all link to the start of their respective chapters -- but that's where they think their bookmark is. With 12 endnotes, I'd be inclined to re-enter them by hand.

Pay attention to Type | Document Footnote Options and Document Endnote Options. You can use them to apply styles to your endnotes/footnotes. These settings don't synchronize between files, apparently. You must do each file separately.

Use the Articles panel for EPUB output. The Book panel controls what order ID outputs the files, but the Articles panel (one for each file) controls how the items within the file are output (or not). Use Object | Object Export Options for items in the Articles panel.

PAY ATTENTION TO HIDDEN OVERRIDES. These prevented several (many many) Kindle Previewer attempts for me. Click the Show Overrides button at the top of the Paragraph panel. You may be surprised at what lights up. Get rid of these overrides if possible -- they prevented Kindle Previewer from being willing to "enhance text" for me or even process the EPUB.

The other posters are absolutely right in that EPUB readers is where browsers were years ago. I got better-looking results from 3.0 than 2.0.1 even though there was nothing interactive in the book... but we were aiming at Kindle, which handles 3.0. Some of the other platforms do not.

Good luck.

I'm testing it in Apple Books and in Thorium (my Windows 10 machine)

The screenshot is the paragraph style I'm using for my chapters and page breaks. This style is also used for my toc.

The short answer is that EPUB doesn't handle either footnotes or endnotes very gracefully, and any kind of split in the document can confuse both the export and the reader on where to place them.

It also depends on which reader you use to view the EPUB, and readers are where web browsers were 15 years ago, each with its own quirks and interpretations. I suspect that's the question Bob is asking here—which reader are you using?

I am not clear by what you mean that a paragraph style was set up to 'split document.' Can you clarify?