It sounds as though Molly still has a lot of ear problems. This is NOT your fault, it's not her fault either. She is probably in some degree of pain most of the time, hence her 'attitude' problem. I have seen this type of situation so many times with Rabbits who have chronic otitis. Some become ultra submissive, some become total bullies. I believe chronic otitis may also cause tinnitus (ringing/buzzing in the ears) which, if you have ever experienced it, is more than a little annoying. I believe Rabbits also get 'headaches' when they have chronic ear disease.
Needless to say the words 'Rabbits' and 'Ear Infections' makes my blood run cold. Purely based on what I have seen over the last 10 or so years.
In all honesty I think you may need to consider separating them. I have always thought this may be what would happen, but I really do NOT mean to sound as though I am saying 'told you so'. It is just having been through such similar problems regarding cases of chronic otitis and all the less obvious issues it can cause I know that if a bond becomes fraught it is very unlikely to improve. Then both Rabbits start to pay the price in one way or another.
Again none of what is going on for Molly and Barney is your fault. It is simply a very unfortunate situation that can happen when one Rabbit has a chronic condition that causes behavioural 'symptoms' as well as the more obvious clinical ones.
Would alternating 'in enclosure'/free range time between the two of them be an option ? So one in/one out. They can interact with each other (or not) through the sides of the enclosure, but Molly wont be able to bully Barney.
Also, what treatment is Molly on for her ears now ? Has she had a skull Xray ? If she has a lot of debris in her ear canals this can cause lots of pressure/pain. It also often means that there is loads of pus behind the debris and until it is cleaned out no topical treatment (eg Canaural) will be of much benefit.
I totally understand how stressful all this must be for you. I really hope that this post will be read as I intend it to mean and not as me trying to say you are in any way to blame. You are most definitely NOT.
(((Hugs))) xx