That's the bug on every KitKat based ROM, I already told you. You haven't actually lost your battery p
ercentage, it's just showing wrong informations.
Just reboot to recovery with your phone plugged into the charger, and then reboot the recovery itself, and your battery should fill up.
And install BetterBatteryStats, let your phone idle during the night, and post the log here, so we can tell you if there's anything specific draining your battery.
Sent from my GT-I9100
I'm running kitkat themed jelly bean.