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I have never used an FTP client that allowed you to drag-n-drop directories within the remote server. It is one thing to drag a directory to/from a server, but it is something else entirely to drag a directory WITHIN that server.
If you accidentally grab a directory due to an errant mouse click, it is very easy to blow away a live website. It is pretty easy to do on a machine that may be saturated and slow to respond. A mouse click and drag can confuse a system pretty easily when it is under load.
It happened to me, and it took the better part of a day to figure out what happened and to fix it. After relating this story to a few folks online, I heard from several that it had happened to them as well. It also happened to me a few more times after the serious one and that was when I put down FZ.
The reason I needed to download was due to a loss of backup. I ended up having to recover the files from a toasted disk.
In my case it was my error, but it just goes to show how easy it can be done. I think FZ should impliment an "are you sure you want to..." style pop up when you are about to do something major.