Issue #1:
Here's my first dilemma: I am building a book with several hundred pages. This book will be printed (won't be an eBook/iBook). I'm keeping each chapter as its own document that I will then collect together as a larger Book at the end. The last chapter will be just for all the book's endnotes. In previous versions of InDesign, I would import the Word document, delete the endnotes out of the "Chapter x" document, and pop them back into the "Endnotes chapter" without affecting the superscripts referencing the endnotes throughout the text. Easy. Now, in cc 2018 if I delete the endnotes out of the "Chapter X" document, the reference superscripts throughout the text get deleted as well. I don't want this. Is there any way to disconnect the superscripts in the text from the endnotes? If I must, I can leave the endnotes in a text frame off the page if InDesign MUST have a reference. Which leads me to my next problem:

Issue #2:
Each chapter I'm working on has multiple sets of endnotes, i.e. multiple side bars with their own set of endnotes that need to be kept exclusive from the general chapter endnotes. In the previous version, before Indesign could recognize endnotes, it would allow me to have multiple sets of endnotes that don't interact. Now, it's one big run-on list of end notes. Example: I have 10 paragraphs of chapter text, with endnotes #1-5 in it. Then, I have a sidebar that gets inserted after that. At the end of the first sentence in the sidebar, there is an #1 endnote that refers to the sidebar endnotes. However, Indesign converts it to #6, because it's the endnote that falls after #5 in the general chapter.

Is there a way to fix this so I can restart the numbers for each sidebar? Can this be done with style sheets?