Thanks for all your help so far. I'm going to give an update on what's been happening.
The day after taking Odo to the vet, we bought some feliway, in a diffuser and a spray. Using an extension cord, we plugged in the diffuser 3 feet from the door, on Marmalade's side. I'm not sure how much good it has done her, but it certainly seems to give Odo more confidence. Whenever he gets freaked out, if we spray the feliway outside of his hiding place, he comes out, when his favorite toy and treats couldn't entice him out. Also, within the week of getting the feliway, Odo escaped from his room 3 times when we were bringing him food. Luckily, the 2 cats didn't have an encounter, as I was able to close him into a different room, but it shows that he's not afraid of her, despite being hurt. I'll keep using the feliway, it may just have a smaller effect on Marmalade, but some effect is better than none.
I continued switching their rooms, but neither cat was very happy about it. Marmalade won't stay 5 minutes in Odo's room, and Odo tends to just hide under the couch or bed when he's switched.
Odo likes to stick his paws under the door to try to interact with Marmalade. Her first reaction was to hiss, and then swat at his paws. It has now progressed to her smelling his paws before hissing, which is at least a little bit of progress.
3 days ago, we replaced the door to Odo's room with one that we had a mesh screen installed in the bottom so that they can see and smell each other much better. Marmalade's first reaction was a lot of unhappy meows, but I was glad that it wasn't hissing and lunging. Odo has been trying to make friends with her by meowing happily at her, and exposing his stomach to her. When he makes sudden movements, she gets freaked out, hisses and hits the mesh, but, she's been slowly starting to stand more movement on his part before hissing. Within the first day of putting in the new door, she was already ok with eating in his presence, even if he is as close as he could be to the door. I'm going to keep them at this stage for quite awhile, at least until Marmalade starts to make some more positive indications to his presence.
I am planning to buy Cat vs Cat soon, thanks for the suggestion. I'm sure it will come in handy.