My favorites list includes regular digital channels and HD channels. The entire list appears intact on my iPad. But my television Contour guide favorites list only shows a small portion of that list...
I have the identical problem. It started when the channel relocation update was installed in my Contour box on June 19, 2018. Cox tech support initially diagnosed the problem as a defective Contour box. A new box was installed and it didn't fix anything.
That's when I discovered that the Favorite Channel information is NOT stored in the box! Cox keeps track of this info in their central computer. Another Cox tech support rep admitted that it is a known software issue and an update will be automatically installed at some later date.
In the meantime I managed to get things working again by programming (selecting) BOTH the low and the high channels; channel 10 and 1010 for example. This also means that you now have twice as many channels on your list.
I have not been able to find an easy way to program the channels as they have a habit of randomly appearing and disappearing. Start out by selecting all channels and then clearing all channels. Program all your channels, low and high, at the same time. Repeat as necessary - it took me about 5 tries.