Describe exactly what you mean by "lose the configuration" and exactly what you mean by "back up".
"Backing up" a DeviceNet configuration means, to me, that you are uploading all of the configurations from the devices into an RSNetworx for DeviceNet project file.
My guess about what's happening is that the DeviceNet Scanner is configured for "Auto-Device Replace", and has a stored set of parameters inside the Scanner's ADR memory.
When you cycle power, the scanner checks the drives to see if the parameter checksum it has saved matches the one active in the drive. Because you changed some parameters, they aren't the same, and the ADR feature re-downloads the old parameters.
To update the parameter sets in ADR memory, you need to reconfigure the ADR memory on the scanner, using the ADR tab in the scanner configuration applet. This involves uploading the current drive parameters then saving a copy of them onboard the scanner. This must be done for each drive, individually.