Just purchased the above recorder and started an
auto-setup. This programmed many digital channels but none were the film or sport channels which I subscribe to.
I could reprogramme any analoge channels manually to any channel above 900 but it seems that I cannot go into the digital channel and alter manually.
Is there a way to do this?

I am slightly confused as there is no facility for inserting a top-up TV card on this model, so am uncertain how you'd decode the signal anyway. To the best of my knowledge you cannot amend the channels manually - all you can do is add additional services or do a complete set-up.

Just to add that my receiver does show all the encrypted channels - but the only two that seem to meet your description are Eurosport and TCM

Assuming you're in the UK, the digital channels for this recorder are Freeview, so nothing that you would (or could) subscribe to. As the other reply says, the EH60D isn't for Top-Up TV (though it does list those channels). You can filter out unwanted channels from the EPG list by using the Profiles facility.