Is he able to come and go from his enclosure freely when he’s getting exercise time? Just checking because if he has to be picked up to go in and out that could be contributing. Adding some hides for him in the exercise area can also help.
It’s true that some bunnies take a very long time to warm up to their humans. I adopted a bun that had become “cage aggressive” at the shelter about 2 years ago and she is just now letting me pet her regularly. Things that can help are hand feeding A LOT, and having each member of the family hand feed him. You can do this with his daily salad and pellets so you don’t end up giving too many treats.
Spending lots of time with him but basically ignoring him are often the best bet. Playing “hard to get” seems to work well for most rabbits.
If he will take food from your hand, you can also try doing some clicker training with him as a way to interact with him that doesn’t involve petting.
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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.