New rabbit owner needs help with bonded rabbit behaviour

[Tanya@]

Im perplexed. 3 months ago I adopted 2 bonded spayed females now 2 and half years old. Recently Eva the dominant has been chasing the other & nipping resulting in pulling clumps of fur. Thankfully there is no fighting however Millie is scared of Eva. To try to prevent further breakdown of relationship, I separated them oner night (Millie can squeeze through the baby gate to escape Eva). Then today I took them for a car ride. After there has been a couple of small chases. My issue now is that Millie seems totally scared of Eva. She runs from her even when she's not being chases & then thumps once or twice. My concern is that this may continue to keep Millie from the hay & litter tray to stay far from Eva. Because Millie escapes their bedroom through the bars of the baby gate I'm thinking of putting grids over the gate. Any help would be appreciated. (They had their health check last week & no issues or illness). Thanks