After the update, do I have to render my whole audiobook again to remove the spoken citations?

No. Open the Audio page for the book and render only the chapters that contain citations. BookyAI keeps the audio of every sentence it has already synthesised, so only the sentences whose text changed are made again and the rest comes from the cache; a chapter re-renders quickly. A chapter that was already rendered is not marked as outdated automatically, so you choose which chapters to render again. If you made a single merged file of the whole book, create it again after re-rendering.