On a FGT where you have two partitions, you can use the following command to see what is your active partition : diagnose sys flash list
You will get a result like below :
Partition Image TotalSize(KB) Used(KB) Use% Active 1 FG-5KD-5.02-FW-build670-160422 253871 45550 18% Yes 2 FG-5KD-5.02-FW-build670-150715 253871 45917 18% No 3 EXDB-1.00000 14866900 39164 0% No
In this example, the active partition is the primary. To reboot from the second partition, the command to use is : execute set-next-reboot secondary
and then reboot the unit (if the active partition is 2 and you want to reboot from partition 1, replace secondary with primary)
If you have a cluster, then you need to look what is the active partition on each cluster unit, use the "exec set-next-reboot" on each cluster unit and reboot each cluster unit.
If your upgrade is from 5.0.11 to 5.2.6 , it seems (see http://cookbook.fortinet.com/sysadmins-notebook/supported-upgrade-paths-fortios/4/) that you can go directly from 5.0.11 to 5.2.6. So as your upgrade can be done in one step, you can go back to 5.0.11 and config used with 5.0.11 using the reboot from the other partition.
If you have an intermediate upgrade step between 5.0.11 and 5.2.6 you would not be able to go back to 5.0.11 this way, only to the previous version used before the last upgrade
