System Settings : Configuring general settings : Backing up and restoring the system
 
Backing up and restoring the system
Fortinet recommends that you back up and restore your FortiManager configuration to your management PC or central management server on a regular basis to ensure that, should the system fail, you can quickly get the system back to its original state with minimal affect to the network. You should also perform a back up after making any changes to the FortiManager configuration or settings that affect the managed devices.
You can perform backups manually or at scheduled intervals. You can also create a backups - called checkpoints - that define a point where the FortiManager and network management is stable and functioning. Should any future configurations cause issues, you have a point where the system is stable.
Fortinet recommends backing up all configuration settings from your FortiManager unit before upgrading the FortiManager firmware.