Generally the hormones don’t abate completely for 4 weeks after the speuter, so she may only just now be feeling less effects from her hormones. Plus, I agree with both the possibility of it being the new male spraying, or your girl marking her territory.
I don’t know if this will help, but you can try changing their litter to Aspen wood, either shavings (which are the only safe shavings) or pellets (sold in bags for birds, but great for bunnies). Aspen absorbs odor about 4x other litters, and we use it with the bunny right near our open kitchen. No smell. If the smell is in any way related to the litter pans for both, that will go a long way in getting rid of basic litter odor, especially of cecals. Those are the edible poos that are very stinky.
It will help once the boy bunny is neutered. I think it will be a temporary problem that will resolve once they are both speutered and bonded. I know it’s hard to take for now. I am very sensitive to smells, too.