When the computer is disconnected from battery power it can forget it's history and any engine/transmission tuning parameters which will cause it to default back to it's baseline setting.

If you're in a state where you have emissions testing, the computer forgets this stuff w/o battery power and you have to go through several drive cycles for the computer to verify everything is working fine.

I wouldn't think there is any risk of hurting anything if you don't mind the computer taking time/miles to relearn what it needs.