We have had a few endpoint that was stuck on disconnected and so far all has had system related issues and after a refresh install of Windows the client worked again.
We tried everything we could think of, like just reinstall Harmony and tried reconnect tool. What we later found was that these machines had other issues with windows update and other system services that did not work.
You can try the reconnect tool first if that fixes it for you.
maketool.bat in the INVOKE folder for SmartConsole, you need the config.dat for the package that is installed on the endpoint.
For R81 it is C:\Program Files (x86)\CheckPoint\SmartConsole\R81\PROGRAM\util\RepWorkFolder\INVOKE