I know this is going to sound a very simplistic/stupid question to most of you but...if I do an automatic reinstallation of channels will i lose my stored programmes?

No.

The only thing that you will lose are any scheduled recordings that you have set up. But retuning does not wipe the hard drive. That is a separate function of the Humax

Thanks very much

Favourites are also lost at the start of automatic reinstallation of channels.