I added chapters to my book and now the endnotes, glossary and discussion guide don't match. How do I update them?

Open the book's workspace. When chapters have been added, regenerated or reordered after the appendices were written, the Appendices card shows an amber note saying the chapters have changed, and the Regenerate appendices button rewrites the front and back matter from the current book: introduction, glossary, discussion guide, endnotes, further reading and the rest. Every chapter's continuity summary is used, including chapters added later, so the new material is covered. The previous text of each rewritten section is kept in that section's Versions. Sections you wrote or imported yourself (for example your own preface) are never overwritten by this button; to rewrite one of those on purpose, open it with Edit and use Regenerate section.