You may want to look at this post: Re: Atlas 550 Loses Config
There is no command to have the ATLAS save the configuration. It is saved as you configure the device. In order to verify if it is a failure of the NV BATTERY, you can run a system self-test. If the results show an NV BATT failure then the Dallas Chip has failed - which means that every time it is powered off it will lose the configuration.
You can download the configuration (via XMODEM or TFTP) so that you have a backup of the configuration and then re-load the configuration when the unit is power cycled and loses the configuration.