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Ah this is a large good set up... maybe what you could do is add an extra hay feeder like this or this toward the other end of the litter box (just tie/attach to the bars of the xpen sort of eye level with the litter box). If they are not vying for the same hay possibly the dominant one will not try to push the other one out. It would be worth a try.
Then reinforce reinforce reinforce for both ... use positive reinforcement. Remind them that a litter box is a good thing by giving a tiny treat every time you see them use it for a while. In you case since one may be bullying the other a bit, give a small treat to both when one uses the litter box (you can use fresh herbs or pellets as a treat not to overfeed).
If you are ever there and see one get ready to go (her tail kind of lifts up like in this video https://www.youtube.com/watch?v=ym7-BBY4ep4) scoop her up gently and put her in the litter box. If you see her make one poop, as soon as you see it place her right in the box so the rest she does in there. Once she goes give that little treat as a reward. This reinforcement if done consistently over time will really help I hope. Place any poops you find back into the litter box together with the bunny to reinforce and if she pees outside use a napkin to blot it and again place back into the litter box.
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PS I must say the stuff you have above is a bit worrisome... if one of the girls accidentally knock the xpen and the things fall they could break their spines...