That's not a problem we've ever heard of before. Joomla even has safeguards in place which won't let a component installation update folders outside of the /components, /modules, /libraries, or /plugins directory, so I'm not sure how JFBConnect did that.
JFBConnect itself (the main component) can not be upgraded from the Update Manager. It can only be upgraded by going into the component itself. When you try it from the Update Manager, you'll simply see an error that the installation failed, but no changes are made to the system during the process.
All the add-ons for JFBConnect (modules, plugins, etc) can be upgraded from the update manager though.
Can you tell me:
* All the extensions that you were trying to update when the problem happened?
* What was the error message you got?
* When you say the index.php file is empty, do you mean your home page is just blank or if you edit that actual file, it's completely blank?
** If the home page is just white/blank, try going into the Global Configuration area of Joomla and set error reporting to "Maximum" and see if a better message appears.
** If the index.php file is actually empty when you look at it on the server, you may need to reinstall Joomla.
Keep me posted on what you find. Again, this is something we've never heard of and I can't imagine any way that JFBConnect could do this, but we'll gladly help how we can.
Thanks,
Alex