Hi,
Update for those interested and hope it can help with others who might have the same issue.
After the vet's advice, we isolated her and started to give her antibiotics in liquid form. During the night we keep her in a plastic container where we held our ducklings the first 2 weeks. She sleeps inside the house.
I had time to observe her closely:
The first night might have been the worst, her breathing was heavy with open beak. Sounds also like she has mucus or liquid inside her throat, noticeable when she takes breaths. At times she would cough like she is trying to get rid of the mucus.
There is however no discharge from her nostrils. She would also make this eating/drinking motion like she was removing the liquid that came up?
She also doesn't want to lay down and is keeping her head and neck high. I believe it might be the most comfortable position for her to let in the air? When she would turn her neck or shake her body she would cough after that.
Last night it was the same but got slightly better around 3 am. She also didn't sleep and if she did it was very little. (I check up on her very frequently).
Apart from the antibiotics we didn't do much, I used saline solution in her nostrils hoping it would help her a bit. I didn't notice any discomfort from her side so believe it didn't to her damage?
I also hand fed her just to make it as easy as possible for her.
What I notice is that she got more violent last night. When I would approach my hand she would pick at it. This might be because of the news we got this morning? Or just wanted to be left alone.
So this morning as a surprise she laid an egg! Very unexpected I would say.
This however rules out she was egg bound right?
Breathing has been a bit calmer for now but still has the occasional cough.
We took her outside, she was searching for food, took a dive in the pool and dried herself like nothing is happening.
It looks like she is getting better so I'm hoping for the best.
I believe now her behavior is that she has a bacterial or viral respiratory infection and not from the possible egg bound or molting.
I hope she is out of the woods now. Going to continue a few days with the antibiotics and keep her separated.

Thanks for all your input!
Nuki