There is a glitch with the ViP scan that can cause it lose old channels. However, that only occurs when those channels are actually coming in, but with a very low signal strength. In that case, it is relatively easy to add the deleted channels back by simply scanning again, or manually adding each channel back. Channels that are not coming in at all do not get deleted from the list unless you manually remove them.
Unfortunately, the Hopper/Wally scan is the exact opposite, deleting any channels that are not coming in, and not necessarily adding all of the channels (that are actually trying to come in) to the list, either. Many of us have been wanting Dish to change the Hopper/Wally scan to act more like the ViP scan, ever since the original Hopper first came out.