Was the cluster configuration in sync before you started the upgrade?
We ran into similar problems, were ISDB entries just got deleted, when doing a multi-step firmware upgrade. This happens when the ISDB is out-of-date or empty.
Not sure if they fixed this in later firmware versions.
What I do is:
- Run Firmware Upgrade
- check if ISDB entries are populated again
- If not: execute a fortiguard refresh (System->Fortiguard, Update AV&IPS Definition)
- run #diagnose debug config-error-log read
- do next firmware upgrade