|This is where you need to be using some sort of version control software/system.
By using version control, your directory structure and contents will be versioned which means that it will be easy to trace and restore when anything changes or moves.
I have seen others struggle with the same issue you are describing and they never came to a solution, however as soon as I started working in tightly version controlled environments what you describe was no longer an issue.
You could create one main repository or a repository for each second level directory - the only downside is that it will take a bit to educate people and set it up but it will allow you control and transparency over actions taken of individual files.
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