@la From what I understand from your post, the device is a remote control. Can it also act work like a gamepad controller ? Because this is what RetroPie recognizes and configures to navigate the Emulationstation menus.

I never tried that kind of remotes, but it should work. Did you configured the remote like explained here ? https://support.myharmony.com/en-in/harmony-experience-with-kodi or here ? http://wiki.openelec.tv/index.php/Config_harmony

Would you mind sharing how you got the Harmony remote working with Kodi?