So i was trying to create a build for XCode with Symlink enabled (for iOS). I just deleted the build folder used before and forgot to switch to another folder when building again and Unity just automatically choose the Document folder (because this is the root folder where i store my project) instead of my project folder. And suddenly, all my files inside Document folder just disappear except for my project folder.
Last time someone reported something like this, it turned out that Unity actually safeguards against that situation ie trying to choose the project’s root folder will popup a “no can do” message box.
On Windows:
I was able to use the project root’s parent folder as a build output, but that didn’t delete any existing files and folders, it just added its own files (making a mess).
Did you check Finder to see what’s under Documents? It may have been a simple misunderstanding because the selection dialog of Unity will let you pick folders only, it won’t show any files inside each folder.
For example, on Windows trying to use “Videos” as output shows none of my video files because the dialog shows only folders on purpose:
When you know that folder should contain all your important files, but you don’t see them, understandably that could cause panic. But the files are still there in my case, I really hope that’s just the same for you. 