Your poor Rough Collie – 11 days in hospital is a long time and it sounds like he did very well to survive such a nasty infection.
Mucoid nasal discharge can be due to many different respiratory associated diseases but in your dog’s case, it is likely to be associated with the previously diagnosed pneumonia and nasal cavity erosion.
Have you taken him back to see your vet? I would strongly recommend that he be reviewed to ensure that the pneumonia has resolved completely and try to narrow down why the nasal discharge is persisting. It may just need a little more time but it also possible that things are not quite yet resolved. Eating well and being playful are good signs of improved health and his intermittent low energy days may be just temporary as his lung’s recover but I would recommend a review of his condition just to be sure.
Also remember that you can always seek a second opinion with a specialist veterinarian, for your Collie’s problems you would need to see an Internal Medicine Specialist or a cardiothoracic specialist. A consult with either of these may be money well spent as they are highly trained in their disciplines and tend to be very used to treating unusual or challenging cases!
I wish you the best of luck with clearing this respiratory disease once and for all!