If, after you flash a ROM and run it, it seems as if the battery indicator isn't tracking battery usage to what you think they should be (i.e., your battery normally lasts 20 hours, but now it's been unplugged for four hours and says 50%), it can be very helpful.
Plug in and charge to 100%. While it is still plugged in, restart the phone in recovery and wipe battery stats. Do not wipe anything else. Restart the phone and, when it is done, unplug and use it as long as you can.
If battery usage seems reasonable, there is probably no reason to wipe battery stats.