What do you mean, rooted?
Do you mean a factory reset of the device?
If so the OS has nothing to do with the battery at all.
A smart Lithium battery is actually 2 parts.
A chemical battery (the battery itself) and a digital battery (the actual charging and calibration circuitry).
These are both independent of the operating system of the device.
The OS (iOS or Android for example) simply pass on the information from the digital battery and display it for you as a battery meter.
If the digital battery is showing an inaccurate measurement, so will the battery meter.
While the handset has a charging circuit with all the fast/trickle and overcharge protection gubbins, this is not controlled by the OS at all.
If it was it wouldn't be possible to turn your device right off and still have it charge ok, which all phones do fine.
All I'm trying to say is that sometimes the chemical and digital sides get out of step from their original settings and doing a full discharge will set the low flag and then a full charge will set the high flag and this should cause your meter to be more accurate.
All this going on inside the battery though, nothing to do with the OS.
http://batteryuniversity.com/learn/a...ry_calibration