I hope someone gives you a good answer, because I’d like one myself. My method has just been to do this stuff little by little. I would also recommend calibre web for interfacing instead of calibre. You can run both in docker, and access calibre on your server from whatever computer you happen to be on. I find centralizing collections makes the task of managing them at least more mentally manageable.
You might want to give an idea of the size of your library. What some people consider large, others might consider nothing much. If it is exceedingly large you’re better off asking someplace with more data hoarders instead of a general Linux board.