tuned efans bad battery

I tuned a friends truck and set up his efans to work but he had a bad battery and we used a jumpbox to power it in order to program it. Fans were working correctly and everything was fine. Then his battery went dead and the fans didn't work anymore as if it didn't save the tune or forgot it because of a bad battery I reprogrammed it and it worked again. But I'm afraid its not going to retain the tune due to bad battery. Needs to just get a new battery. Has any one had a similar issue with a crap battery?