The EMS installation includes installation of Microsoft Visual C++ (VC) 2015. If the server already has a newer version of VC installed, the installation fails. See VC++ 2015 Redistributable installation returns error 1638 when newer version already installed.
If you have a version of VC installed on your server that is newer than 2015, uninstall VC before installing EMS.
When managing more than 5000 endpoints, install SQL Server Standard or Enterprise instead of SQL Server Express, which the EMS installation also installs by default. Otherwise, you may experience database deadlocks. The minimum SQL Server version that FortiClient EMS supports is 2017. See the FortiClient EMS Administration Guide.
A split tunnel configuration that functioned in FortiClient (Windows) 6.4.1 no longer works after upgrading to 6.4.9, unless you have configured a per-tunnel configuration in EMS.