While neutering does significantly decrease, and in many cases completely eliminate, the onion-y poops, they can still occur. My female rabbit still does it even though she is spayed, and I am sure a big part of it is because firstly, she had been introduced into my home a year ago so it was new and smelled of another rabbit, and secondly, she and that rabbit are not bonded, so the necessity to spread her scent may still be strong, even though she is spayed.
Some rabbits are more sensitive than others when it comes to others “invading” their space and needing to re-mark it… is my thought. It’s good that they are staying in the litterbox though!
Unfortunately, I do not have a solution– just normalization that it is still typical for a fixed rabbit to have those territorial poops.
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.