FortiManager v5.0.0 introduced a new hard disk drive partition layout which is required for optimal usage and performance. Following an upgrade to FortiManager v5.0.0 or later, a backup must be made and then the disk must be reformatted with following command:

A format will erase all local logs, and FortiGuard database information. Backup any local event logs that you wish to keep. The FortiManager will then need to re-download all of the AV/IPS/AS/WF objects from the FortiGuard Distribution Servers (FDS) which may take up to half a day. During that time managed devices will not be able to obtain these services from the FortiManager. You should configure devices to point to a backup FortiManager or the FDS for these services.