I’m so so sorry for your loss. 🙁
It’s really good he was able to spend time with her body and say his goodbyes. Bunnies that are able to do that usually handle things quite well (sometimes better than we do honestly).
Her scent will naturally decline over time, he will be able to tell between “fresh” and “old” smells, so I wouldn’t worry about removing her scent or anything like that. I would keep his area just the same for now, so it’s not so many changes all at once.
All you can do for him now is spend extra time with him (even if its just hanging out in the room with him), and make sure he keeps eating and pooping. He may be a bit more quiet than usual, but if he stops eating he may need to be syringe fed. If you have other bunnies, he might like seeing them as neighbors if you notice he starts to get depressed. Some bunnies also like having a “stuffy” to cuddle with.
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The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.