Can I give the AI instructions for every chapter when I use "Regenerate all"?

Yes, from version 1.9.23. In the "Regenerate all" window, type them in "Instructions for every chapter (optional)", for example: "Do not reveal that Tom is John's son before chapter 3." Every chapter receives them, together with the instructions you gave that chapter on its own. The AI is told which chapter it is writing, so an instruction about some chapters, like "not before chapter 3", applies exactly as it says. Without the "Keep these for this book" tick, the instructions are used for this regeneration only.