Ok, just to understand this fully:
BBC one HD, BBC Two HD, ITV 1 HD, Channel 4 HD and Channel 5 HD are officially in the secondary section/bouquet.
You are implying/suggesting that:
The user has hidden this section, the all bouquet does not contain the channels that are officially in the hidden section.
So how come the the Entertainment bouquet shows the channels that are officially in the hidden section? Can't this logic be applied to the all bouquet?