My blueprint file has sections BookyAI does not know. Are they lost?

No. When you load a blueprint in version 1.9.18 or later, BookyAI shows a note such as "2 sections of the file are not part of the blueprint format" and names them. Those sections are kept: they go into the book's Codex as notes that the AI reads while writing. The keys BookyAI understands can be written in any style (must_include or mustInclude), nested under "book" or at the top level, and numbers in front of chapter titles ("Chapter 3: ...") are removed. If the file has no chapters, BookyAI says so and plans the chapters itself from the rest of the blueprint.