This issue appears to be a bug. Others, including myself have this issue."homeron" said:
My default Favorite List resets nightly and occasionally (less recently) channels disappear from my Favorite List.
When channels disappear, occasionally I have to change at least 2 channels in my Favorite List for the changes to save.
I wish more people experiencing this issue would report the issue so it would get prioritized at Dish to get resolved.