Vector dbs work by fetching segments that are similar in topics to the question, so like "Where did <Character> go after <thing>" will retrieve segments with locations & the character & maybe talking about <thing> as a recent event.
Your question has no similarity with the segments required in any way; & it's not the segments that are wrong it's the way they relate to the rest of the story
Which makes me wonder if the opposite, but more laborious approach might work - request it identify all characters and plot themes, then request summaries of each. You'd have to review the summaries for holes. Lotsa work, but still maybe quicker than re-reading everything yourself?
But I've started experimenting with the second part, of sorts, not to find plot holes but to have it create character sheets for my series of novels for my own reference.
Basically have it maintain a sheet and feed it chunks of one or more chapters and asking it to output an a new sheet augmented with the new details.
With a 100K context window I might just test doing it over while novels or much larger chunks of one.
I feel this is mostly a prompting issue. Specifically GPT-4 shows surprising ability to abstract to some degree and work with high-level concepts, but it seems that, quite often, you need to guide it towards the right "mode" of thinking.
It's like dealing with a 4 year old kid. They may be perfectly able to do something you ask them, but will keep doing something else, until you give them specific hints, several times, in different ways.
Contriever is an example of a strong model to do that yourself. see their paper too to learn about the domain. https://github.com/facebookresearch/contriever