Not really sure from your post what your setup is. Is this combined TV and satellite feeds running through a multiswitch and then feeding the
Sky HD boxes which link direct to TVs, or are you running through an HDMI controller?
If it's the latter, it may be that the controller doesn't support HDCP and the
Sky HD box will not send a signal to it via the HDMI. I had a customer with precisely this problem last week, although it had been OK previously, but he started getting black screens with no audio only, he now has to watch via the scart connection.