This is a very interesting problem and I don't know the best solution yet.
I see this happens for most of the tools when the amount of information/data (notes, photos, etc) surpasses a certain threshold that I can handle because (1) I forget the past work so I forget how to categorize, connect, and retrieve certain information or (2) a way of thinking grows over time so I might try to use another method to organize which messes/disconnects the past work. I think that "disconnection" or "isolation" of information is a problem. It's all about "entity" and "the relationships".
Search can solve this issue. The Internet is a massively interconnected place via hypertext thus search helped us access relevant information. The connection helps search engines assess their quality. Citation works in a similar way.
In the case of note-taking, bi-directional linking might help us understand the relationships among them but I don't know if and how it can really help me access needed information faster and leverage them easier and more effectively.