Unfortunately the method Harmony is currently utilizing uses the legacy SmartApp/DTH/Groovy implementation which is going away essentially any day now. This means your ability to control scenes directly on your Harmony remote via virtual switches in the manner you currently are doing it will no longer work.
There is a Logitech Harmony Bridge Edge driver ( https://community.smartthings.com/t/edge-device-simple-harmony-bridge-alpha-testing )that somewhat solves the issue, but unfortunately won’t allow you to directly control Scenes from the remote. You can, however, have SmartThings run a routine that activates a Scene when a Harmony Activity runs. Or you could create a fake device (like a tv you don’t really have) as a Harmony Activity that then is activated via the remote.
Tons of information on this over on the Harmony Bridge thread, let’s not derail this thread too much.