[Q] Flashing ROM's at less than 100% battery

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http://forum.xda-developers.com – Will flashing a ROM with less than 100% battery harm anything? My wife's phone is still having issues with the NEWsense rom after getting a new battery from sprint. I flashed NEWsense while the phone was charging, at the time of the flash it was at roughly 45%. When charging, it will say it's charged to 100%, but after 3 hours of light use with wifi on, it's down to 27% already. Is this something the battery calibration option in the NEWsense control panel would fix? Or is wiping battery stats the best way? I could always charge to 100%, then re-flash the rom. I guess I'm just lost (HowTos)