Like Bill Williams, I have experienced over-writing the wrong index.html file. It's a pain, as you want to have them in your directories for usability, but if you do you are always at risk for overwriting.
For a while in my engineering career with NASA, I was the webmaster for our office web site. The site had grown quickly as government agencies had been directed to put as much information as possible on the internet (this was the mid-90s). Consequently, I had many sub-directories containing index.html files.
One day I uploaded the wrong index.html file to my root directory, i.e. the home page! I was frantic and had not yet made a reliable backup. Big mistake!! So I had to start from scratch and re-create the home page! That was education enough. I now make a copy of EACH AND EVERY index.html file, name it index.txt, and place it online with the other one (and of course I also keep meticulous backups). And I am religious about doing this with every root directory and sub-directory on every web site I create and maintain. It has saved my rear end a couple of times since.
Backing up your website is an important solution to this problem. It can be a pain and tedious, but it will, as Bill says, "save your rear." Another option to look into is a tool like Dreamweaver that does the uploading for you.
