Will BookyAI overwrite a section I added myself when it writes or regenerates the front and back matter?

No. From version 1.9.24, sections you add with "+ Add a front matter section" or "+ Add a back matter section" are yours: BookyAI never writes or regenerates them by itself, not when it generates the front and back matter and not with "Regenerate all". The only AI text that ever goes into them is a draft you ask for with "Draft with AI" in the editor.