It sounds like he enjoys the hay more when presented in the litter box, which, in a way might be more “natural”, like foraging and scavenging for the best hay pieces on a dirt floor. I can also imagine that with a hay feeder, the rabbit might be smelling a particularly good piece of hay, but digs and digs to try and get to it, versus when it’s in the litterbox, it’s relatively easy to smell hay and get to it since there are no restrictions. One of my rabbits occasionally digs out hay from our one hay feeder to get to a piece of hay in the back of it.
Is there anyway you could remove the two smaller hay feeders and make it another litter box area? This might be one of the many times rabbit care involves negotiation with your individual rabbit’s inclinations and preferences.
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.