Hi there!
Can you describe your set-up a bit more clearly?
Also, how long have you had your bunny, and is he neutered?
Most bunnies HATE being picked up. He could have been tolerating it because he was scared of his new surroundings! Are you sure you were seeing binkies? When my rabbits are made at me after nail trims they often “kick dirt” at me, where whey flick their legs out behind them when they run away.
Ideally, you want a set-up where they bunny can come out of his pen/cage on his own, then run back in when play time is over. The pen/cage should be your bun’s “safe space” that they retreat to. If you only remove the bunny from his pen for medical reasons, he will know that is is private space and will be happy to return to it after play time.
Two ways to get my buns back in pens:
1. Feed him when it’s time to go in. If he is on a restricted pellet diet (which he should be!), he will probably bolt in when he heres the pellets his to food dish. You can also do this with veggies or a small treat (1 raisin or a tiny piece of banana). My buns go crazy for basil as well! As for training, you would not “spoil him rotten with failed attempts”, because he would only get the reward when he did the behavior you wanted.
2. Clap and “shoo”/herd him back in! Again, this only works if he can hop in on his own! If your cage is elevated, you could add a ramp. More timid bunnies will easily run in, other times you need to give them a gentle shove!
It sounds to me like your bunny is happy, because chewing and thrashing is normal bunny play time behavior! My buns love throwing things around, and destroying cardboard is a great, safe activity for them. They are really more like dogs than people realize, so they need chew toys and places to dig! If he is keeping you up at night, just give him quieter toys at night, like willow sticks, grass mats, etc. I have to remove my buns’ cowbell at night, or I would never get any sleep.
For the litter, wood shavings are not great, and encourage digging. Try switching to pelleted pine litter (like feline pine), which can be purchased cheaply as horse stall bedding or wood stove pellets. Binky bunny sells a wire mesh screen you can put over the bedding to prevent digging. Add a layer of hay and you will have a happy bunny.
Also, just a side note, Kale, spinach, and parsley are all high in oxalic acid, so should not be the only veggies fed. Together they should make up about a 1/3 of leafy greens fed, and should be rotated! You could add in some romaine, cilantro, basil, carrot tops to round it out. He could be turning his nose up at them because he needs more variety.
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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.