Logitech has a forum just for programming Harmony's. I'd go there next.
I have a Samsung BD-J6300 3D Wi-Fi Blu-Ray Player (2015 Model)
and have an HDMI cable from Blu-ray out to Receiver HDMI DVD in. And a HDMI between Receiver and Top box. The only way I could get sound while watching a DVD was to set the input selection to "CD". OK, so I reprogrammed my Logitech Harmony one to "input CD" instead "input D" and it works fine when I first select watch DVD then it automatically changes from CD input back to DVD input. If I hit the help button it changes it back to CD input. Any suggestions?

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