The best way to avoid Fortinet bricking itself after an update is to completely clear the unit prior to upgrade and upgrade the unit from scratch.
From around OS version 4.0 MR3 Fortinet have recently changed the way their units:
- Store the firmware image
- Store dynamic data (e.g. DHCP Leases, Logs)
- Store the bootloader
As a result firmware upgrades using the GUI to update the from prior firmware versions to the current MR3 patch level will result in a unit that has a very high chance of failure upon future remote firmware updates. Doing the below procedure ensures that all of these are up to date.