What does it mean that refactoring ideas improves thinking?

Restructuring your notes restructures your understanding.

Example: You have a note titled 'Project Management Best Practices' that's 800 words long. It covers estimation, stakeholder communication, and risk mitigation — three distinct ideas tangled together. When you split it into three atomic notes and rewrite the connections between them, you don't just reorganize the text. You discover that your actual insight is about how bad estimation causes stakeholder mistrust, which creates the very risks you were trying to mitigate. The restructuring revealed a causal chain that was invisible in the original blob.

Try this: Find the longest or most tangled note in your system — the one that tries to say too many things. Read it once. Then decompose it into 2-4 separate atomic notes, each expressing a single idea. Rewrite the connections between them. Notice what you understand now that you didn't before the split. The difference between your understanding before and after is the cognitive value of refactoring.