I've noticed that whenever a file with links is duplicated on a different server, the copy will link to the images of the original file instead of the ones in its own folder if it can. If those images are modified in the copy, the changes will also appear in the original links instead of the right ones.

This is a huge problem, because what the user think is their most recent version of a work might not actually be at all, which can lead to very serious mistakes, and as far as I can tell it's been going on for some time…

The people that complain about their links going black might experience this problem without knowing it, because that happens on my duplicates when I cut the access to the server where the original is: the duplicate file is searching for the original links and doesn't find them, so it assumes it doesn't have any links, even if its own link folder is right beside it. It's only after closing and reopening InDesign that it finds its own links.