I edited some chapters by hand. What happens to my edits if I press "Regenerate all"?

From version 1.9.21, "Regenerate all" writes every chapter again from the outline, so edits you made by hand to those chapters are replaced too. They are not lost: before a chapter is rewritten, its current text is saved in that chapter's Versions panel (open the chapter in the editor, then Versions), where you can read it or put it back. If you want to keep your edited book untouched, choose "In a copy of this book" in the Regenerate all window: the new chapters are written into a copy and your book does not change at all.