An update that addresses an issue where a players' Badass Rank resets, (also heads, skins and Golden Keys) and allows the restoration of lost Badass Rank has been released on PC, PlayStation 3, and Xbox 360.
This update contains a new function that scans your character data upon load to make sure that you have the proper amount of Badass Rank based on challenge completion.
The way we detect the loss is by scanning your save data to determine how much Badass Rank each character should have and then comparing that to your total Badass Rank. Each character is scanned individually, that's why we ask you to individually load each characters.
If the total Badass Rank is less than what a character's save data indicates it should be, then it's restored. But if the scan indicates that none of your characters should have a Badass Rank greater than the current total, then it won't be restored as the system is unable to detect the loss.
We'll be making further adjustments to the functionality in future updates, but until then, if you feel your progress wasn't properly restored, please open a ticket so that we can investigate further.