I was updating a website (a simple website that grew way too big) on a server 'on the fly', no website is down for maintenance notice here,
I'd downloaded all the files and was deleting the old files from a root directory,
I selected files to delete across two screens in the file manager and watched the deletion, as the server tools file manager kept deleting beyond the files I had selected and proceeded to delete all the directories of my new installation. Ahhhh!
It just kept going up the screen. Ahhhh! Ahhhh!
It killed all my permissions, almost everything ! 1000's of pages.
I fired off an email to the admin of the server, but they said 'huh !'.
So I to quickly download an FTP program and was able to reload everything in about 1/10 of the time it had had taken me to painstakingly upload them using the server tools supplied.
Nothing beats a local backup.
Last time I use server tools.