Oh dear, poor thing. 🙁
Just a word of caution, if the run was that easily tipped over by a dog, it isn’t safe for her to be in unsupervised in general (you may have already come to this realization). Wild predators can and do attack rabbits (especially birds of prey, foxes, etc.).
Although this could be related to the attack, it would be good to rule out other possible reasons for the loss of habits. How old is your bunny? Is she spayed? What is the litter box set-up like? In other words, how big is the box, is there any other bedding in the cage, how big is the cage, etc?
I would also mention this to the vet in case there is a possible injury they missed.
In the meantime, puppy pee pads can be a game-changer and help with the smell etc. as long as your bun doesn’t chew them.
Ruling out a medical cause, or unrelated cause (such as hitting puberty), I wonder if being threatened in that way triggered her to want to reclaim her territory. If that is the case, things should go back to normal over time, but I would want to rule out medical issues first, then go down the list of other possible reasons.
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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.