I have a Harmony Elite Hub and Roku Ultra that had been working fine until recently. I noticed that when I am on the Harmony activity I have called Watch Roku, many of the Roku channels are no longer there on the remote, just numbers. Some icons are still there. In checking further, it appears that the Harmony Hub no longer knows which channels are on my Roku. If I edit the Roku channels directly, the iOS app no longer knows about my Roku channels, which was not. Problem in the past.
In my case it was Harmony Companion not syncing with Roku Ultra after a house move. The "fix" turned out to be to disconnect the ethernet cable to the Roku, do a setup with it connected wirelessly to the same network as the Harmony. Then the commands all worked AND I was able to reconnect the ethernet cable to Roku after that and it continued to work.