Should the phone be fully charged before flashing a rom?
It's just because, under some circumstances, flashing can take a while.  You really don't want your device shutting off while it's being flashed; it can brick the device.

The calibration for the battery is stored, yes, but usually it gets adjusted within a few charges of the phone.  It might be a little inaccurate for a while, but it's not a major concern.