We have automated reinstallations/upgrades using Microsoft Configuration
Manager. It's just a script that removes FCT, reboots, install FCT back
and reboots once more. AFAIK the process is not necessary to have
running on the servers.
I have reported this same issue to Fortinet as well. This comes up
randomly every now and then, when we are upgrading FCT to new version.
We haven't found any other solution than to perform a "clean install" -
remove old FCT version first and install...