I used Regenerate appendices and it overwrote sections I had written by hand. Can I get them back?

Yes. Since version 1.9.3, every section that Regenerate appendices rewrites is saved first in that section's version history. Open the book's workspace, click Edit next to the section in the Appendices card, click Versions, pick the version dated just before the regeneration and click Restore. Do this for each section you had rewritten. From version 1.9.4 this cannot happen by surprise any more: Regenerate appendices shows a confirmation first, sections you edited by hand are kept by default, and a copy of every current section is saved to a backup folder before anything is rewritten.