Reading is a write operation
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Summary
Every serious reading session changes the reader's index, not just their memory. Designing for that changes what a reader should store.
The observation
When I finish a difficult chapter, the artefact is not a highlight. It is a rearranged sense of which of my earlier notes were wrong. The reading wrote to the index, not to the page.
Why tools miss it
Most reading tools model annotation as append-only: highlights, margins, exports. Nothing in the model expects an old note to become false.
A reader that took this seriously would let you mark a previous note as superseded by this passage, and would keep the trail.
What I would try
A single verb — supersedes — attached to a note, pointing at another note. No folders, no tags. Just a directed edge that says: I used to think this.