We've had this problem for a while in terms of handling a single document that appeared in multiple locations on the site.
(IE, you want the Budget on three different pages, but you don't want three different versions of the Budget floating around).
The problem we'd run into is that we wouldn't know which files were updated and which weren't, because if you loaded a file through the Drupal user interface, it would create a brand new document, instead of updating it.
We wound up having to do a lot of hardcoding to files, which is AWFUL, especially, if your files are way down on the site hierarchy.
I'm not sure who else ran into this problem, but I think we came up with a solution - the elfinder module.
It allows you to use the link tool on your text editor to link to files directly on the site from a pre-determined folder. Even better - with elfinder you can also create folders and load up new documents.
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Comments
That looks like a quite
That looks like a quite old-fashioned solution; I remember similar modules from D4.x days. Did you try File Entity? I see there's now a File Entity Revisions module, which seems to exactly fit your problem.
A draggy-droppy file manager is a perfectly fine solution if all your users sensibly name and sort their files. I've never been in that situation, myself. So while File Entity is a more complex solution, you can at least force people to store the document metadata in fields, and find what you're looking for with a view, so it doesn't matter so much when someone uploads 'bobs-new-version-of-that-file-jane-emailed-the-other-day.docx'.
(Disclaimer: I've been away from full time Drupal dev work for over a year, so my brain is increasingly obsolete.)