I had the same issue when trying to use the downloaded Deployment Package to update our customer FortiClient estate from 6.2.7 to 6.4.5 directly, or via Microsoft Intune (customers setup).
I got around it by using Deployment & Installers --> Manage Deployment in EMS (6.4.4). This meant I could push the update to endpoints and prompt the end user to "Reboot Now" or "Reboot Later".
There are other options within the deployment configuration to "Start at a Scheduled Time", "Reboot When No Users Are Logged In", etc... but I haven't tried any of these.
Just be aware that one the update starts, the endpoint becomes Un-Managed in EMS until the end user reboots. Many times I've had end users selecting "Reboot Later", then not rebooting (or just shutting down) till the end of the day.
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