So she's either upset they're separated and 'protest' peeing, or she's not and trying to mark the boundaries of her territory so he knows to stay out. You can try waiting it out. She may settle down after several weeks. Though I would recommend putting down a waterproof floor barrier for now, to protect your floor.
Disposable puppy pee pads work fairly well, provided your bun isn't prone to chew them at all (digestive blockage risk). Washable puppy pee pads are an option as well, but could be semi expensive. A tarp, vinyl cloth, or thick plastic sheeting may work if she doesn't try and chew holes in it, and is relatively cheap. Sturdier, chew resistant, but more expensive, would be to put down a cut of lino (vinyl) flooring. Whatever you use, make sure it's going to be safe for your bun if she's prone to chewing.
You could try putting litter boxes down next to his pen in the spots she most often pees, to see if she'll use those instead. Sometimes it's just about having litter boxes in the right place(s), where a rabbit has chosen to pee. When rabbits are separated by a barrier, that spot is often directly opposite the barrier, of the other rabbits litter box.
If those options don't work, you may need to block complete access to the room, shutting the door, or a baby gate may work. If this still doesn't resolve the issue, you may need to follow Blue Eyes suggestion of restricting her space until she reestablishes good litter box habits, then gradually expanding her space again, as she maintains those habits.
https://rabbitsindoors.weebly.com/litter-training.html
Lastly to consider is a potential medical issue like a UTI. But this is less a possibility if she is consistently peeing in certain spots, as opposed to random spots, and getting a wet bum from dribbling urine.
