Will Regenerate appendices overwrite a section I edited myself?

Not by default. From version 1.9.4, whenever you save a front or back matter section from the editor, restore an older version of it, or change it in the workspace, BookyAI remembers that the section is yours. A full Regenerate appendices keeps such sections as they are. If you do want them rewritten, tick "Also rewrite the sections I edited by hand" in the confirmation window. To rewrite a single section on purpose, open it with Edit and use Regenerate section; after that the section counts as BookyAI's again until you edit it.