Thought I'd draw a quick link to this as it's bound to catch a few folks out.

Joomla : WHM Migrate - configuration.php wiped (TIP)

Joomla installed on an CPanel server and you wish to move it to a new Cpanel server so you arrange (or DIY) the migration using the Migrate or Transfer account tools provided in WHM. WHM handles it all, hopefully and reports a success and you think great...

Visiting the website suddenly starts bringing out erratic behaviour and suddenly the site is non responsive.
I was able to get into the administration section, and then any changes I made to ANY files (configuration.php, virtuemart, etc...) all resulted in a wiped file.

In my case Cpanel has obviously re-assigned a bunch of NOBODY (apache) owned files back to my actual user and this took me over the disk space quota for the account. Net result, CPanel just refuses to write any more data to the account and thus wipes files.

You can either get your disk quota increased to cover the excess or start removing files you don't need... Once you've done this and got yourself back under quota you're sorted..

This applies equally to any site using script that creates or writes files and is error'd out by the quota limit.