I’m sure everyone working in office 365 has this problem to some degree. My (pessimistic) guess is that Microsoft is aware of these problems and in stead of solving them in SharePoint itself, they create more programs to help organising. Like now you can find your files through Bing connected to your workspace (which is just to try and get people to use bing?). There is also delve and such that shows you what you last worked on regardless of its location. And soon we will have the AI co-pilot, which I’m expecting will make things even worse since it will grab anything you have access to and not bother with original context. I don’t know what the endgame is here, maybe make people and companies dependent on these kinds of programs?