The Gearbox Software Forums have complaints from Borderlands 2 players who have had their Badass ranks reset to 0 and have lost the accompanying perks (thanks Eurogamer). Gearbox's Chris Faylor says they are looking into this:

Thanks for all the reports and specific details, folks. Our engineers are looking into this, and the information you've provided has proven to be a great resource while we investigate. At the moment, it seems to be a fairly rare issue and we'll keep you updated on when we resolve it.