To condense the excellent advice above a bit:
The way to get changes made on FGT into FMG is a two-step process, consisting of retrieving the configuration, and then importing the policy:
Retrieving the config gets all changes made on FortiGate into FMG Device Manager, and importing policy gets all policy/object changes from Device Manager into the ADOM database.
-> system setting changes (interface stuff, local admin stuff, etc) are not part of the Policy Package; those changes can be synced with just a config retrieve (if FGT does not update changes automatically to FMG, which it should by default after the admin logged out on FGT)
-> policy (or related object) changes would also be synced to the Device Manager component automatically or via config retrieve, but any install from a policy package will overwrite them
Please be aware, if you have not pushed ANY installation from FortiManager as yet: The first installation will contain a lot of deletions, as FortiManager removes any objects (addresses, users, groups, services...) that are unused, that is, not relevant to any policy or other configuration directly or indirectly.
+++ Divide by Cucumber Error. Please Reinstall Universe and Reboot +++