I think I found the solution, by accident. Hold down the Power button on the OEM remote and the TV will Restart. I think that was the fix. Don't worry, this is not a hard reset so it leaves all of the TV settings unchanged.

I can't be sure, though, if this is what actually fixed the problem. I was on the phone with Sony support trying to get an app to work properly and the tech had me do a bunch of other stuff, too. One of them was to go to Settings, then System, then Initial setup, then Continue, then scroll down and tick the box Agree to all. I'm not sure if this is necessary to fix the problem with the Harmony remote, but it may be.