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Has she been marking more - chinning etc since Pooker's departure? She could be thinking..."Okay, this place is now mine all mine!" and off a marking she shall go. If that is the case, then she could be using her anal scent glands to scent her poos too. And IF that is the case too, then that should stop in a few weeks, and she should be back to her regular sweet smelling bunny self.
Let me know if she's still smelly in couple of weeks.