I had similar experience. While ago I was restructuring my dropbox folders by moving files around and stuff.
The way I use dropbox is that I normally would just dump any files into the dropbox home folder and not give a second thought afterward. However, this became a problem after I got a new computer and discovered that redownloading all the files from dropbox will take some time.
I decided to move all these files in dropbox home to a separate subfolder then selected to not sync that big subfolder. This was a mistake, since I did this on my new computer, which was still downloading files at the time. Dropbox then created a lot of empty folders with familar names with nothing inside and tricked me into thinking that everything is backed up.
To be fair, there was a warning popup saying I just deleted a lot of files, but I had no idea what it was saying since all the folders were still there.