Virgin Media are moving various channels to a new compression technology which uses less space on their network. When they move channels about on their network (I mean behind the scenes, not the channel numbers you see on the Guide) an unfortunate side affect is that it unFavourites them.
When moving channels over to this new technology some channels need moved behind the scenes, others don't, so this unFavouriting hasn't been happening with all these changes.
In theory the only change the customer will notice is that recordings take less space, in practice there can, in certain circumstances, be this side affect.
The short answer is sadly you just need to reFavourite them, and keep an eye on the rest of your list as Virgin are only about two thirds of the way through this change. They are currently changing on average about 10-20 channels a week.