The easiest solution to this is to stuff the heading into the chunk. The heading is hierarchical navigation within the sections of the document. I found Azure Document Intelligence specifically with the Layout Model to be fantastic for this because it can identify headers. All the better if you write a parser for the output JSON to track depth and stuff multiple headers from the path into the chunk.
Instead, completely transforming the text into a dense set of denormalized “notes” that cover every concept present in the text seems like it would be easier to mine for answers to user questions.
Essentially, it would be like taking comprehensive notes from a book and handing them to a friend who didn’t take the class for a test. What would they need to be effective?
Longer term, the sequence would likely be “get question”, hand it to research assistant who has full access to source material and can run a variety of AI / retrieval strategies to customize the notes, and then hand those notes back for answers. By spending more time on the note gathering step, it will be more likely the LLM will be able to answer the question.