Such an unfortunate situation for you!
My first thoughts go to questioning if your female actually was spayed at the shelter OR if it was an incomplete spay. 3 months old seems too young for them to have done this, although some shelters do infantile spays! Im not certain how common that is. Did you receive a spay/neuter certificate for each of them? That she started the chasing a few months after you bringing her home does fit with the age a female rabbit would normally be becoming hormonal, if intact.
I just think for them to have a falling out like this, that there could be some hormonal or other health issue at play.
If not that, has there been any other significant changes at home that could have upset their bond? Any new pets?
It might take some work but it’s not impossible to get them back together. You can also create neutral space. For instance, block of the bathroom and de-scent by washing with diluted white vinegar. Or setting up an ex-pen with a tarp or some other temporary flooring. However, I strongly recommend finding out if Artemis is spayed before proceeding with any bonding work.