As puds11 has said, rabbits are tricky because, being prey animals, they tend to hide symptoms until situation is serious.
The vet's advice is very concerning but it's good that he has perked up loads! He may just need a little more time to get over the operation (although, don't want to depress you, but think the vet would have said that if it was the case). My two female rabbits were neuteured fairly recently and it took them four or five days to recover from the op.
If he is sitting still, and is cold, with ears flopping (it's very obvious when a rabbit is out of sorts) I agree that he may be in pain and in need of some more medication.
He will need to see the vet again urgently if he:
- does NOT eat or drink for a prolonged period of time. (It is very important that rabbits eat continually or else they can get statis of the stomach which leads to further serious complications.) They can also dehydrate quickly.
- is NOT passing droppings or his faeces are watery
-is mouth breathing or (is having difficulty breathing) or his tongue or lips are blue
All vets have a 24hr emergency service so don't feel worried about calling them on a Sunday if necessary.
I think I would continue to keep him separated from his companion, in a calm, slightly dark warm space with lots of hay with access to food and water (maybe a cardboard box full of hay which he can retreat in to), where you can easily monitor him and his input and output of food, drink droppings etc, and leave him to recover but keep checking on him every 30 mins.
If things haven't improved over 24 hrs then I'd go back to the vet.
Once healthy, you may need to focus on the dynamic between him and other rabbit ie if two rabbits hate one another then the health of the submissive one may suffer. It might be necessary to organise a swap. Or to get the companion castrated/neuteured (depending on gender) and then perhaps to separate and re-introduce.
The Rabbit Welfare Society has loads of advice and information available here. Look under 'advice' and have a look at info leaflets in pdf format.
Good luck! It is so worrying when one of your furries is ill!