Hi Matt-
Your experience matches mine and my conclusions are the same: other than if you are writing in InDesign, CC2018’s Endnotes are very limited. If you are importing Word text with Endnotes and need to break the link to the notes, you’re better served by staying with CC 2017 or you’ll lose all the refs in the text.
Like you, I import Word text with Endnotes written by other people. I do all cleanup and applying of styles, both paragraph and character, in Word. I then place the Word file into my InDesign template. My usual practice is to open the Endnotes in Word, copy them, then paste them at the end of the article or, into a collected Notes document for books where all the notes to the chapters appear together at the end of the book. They are not linked, but that is OK for what I do. I then delete the original endnotes, seen as the copy I placed at the end of the document is styled.
Finally, something that may help you: you mentioned that “In most of the books, these endnotes get moved to a section at the end of the book where they are listed by chapter”. Presumably the headers of the pages of this “Notes” section say something like “Notes to pages 00–00.” If that is the case, I worked with Peter to develop a script that will go through the pages of your chapters and populate the headers of your Notes section with the appropriate page numbers. Saves somebody from having to leaf through all the pages to determine what notes fall on what pages. You can find the script here: https://www.kahrel.plus.com/indesign/endnote_running_headers.html and you can find a detailed walkthrough of how to use the script on my website here: https://mackeycomposition.com/resources/
Happy to help out if you have other questions.
