Scared Doe? Protective Mom?

I bought 6 Silver Fox buns from a local guy who bought them for the school he works for but apparently the mom wasn't a good mom and he left the buck in the cage with her and he played mom? Really confusing yeah? Ok let me try to explain. Upon arrival at this place I seen two pretty big hutches and at least a foot of hay soaked in poop and pee... These hutches were filthy... Ok so we're walking up the small slope to talk to this guy about the rabbits he was talking a bit and then said something about babies and he opened the front of the cage and I seen just how bad is was inside. It was filthy, But there was three babies about 2 weeks in a box a terrified mom shoved up in a corner and a dad hovering over the kits. We got all the buns loaded up in the car in 2 smaller cages (Not much smaller it barely fit in my car (I only had 1 cage in my car the other went in my friends jeep) We took the bunnies home and got the trailer hitched and recruited more help. While we were there I seen the does back was pretty messed up and she had a serious ear mite issue. Now I've been putting plantain salve on her back and these "Miracle Oil" drops that is a 100% natural mix of a few bun safe oils. I took her box out today seeing as she is in the bathtub of our house because it's been windy and the hutches aren't the best *On saw horses* She seems terrified since I took her box out. I think it's where she may have hid from the buck... But she now tried to cover the babies sometimes, but other times she hides in a corner terrified..

Give her time, she came out of horrible situation
It is too soon to determine her long-term temperament

Well she obviously don't like having drops put in her ear but who would... She is probably my easiest rabbit to pick up and hold unless she is outside then she kinda acts panicky. Her ears are much better as well as her back! I found a good few more scabs hidden in the fur as I was putting salve on it. It's crazy how messed up she was. I've kept her in the bathtub of my house for a few days and a bunch of people were in and out all day using the bathroom and hanging out with her. I changed the towels twice a day once in the morning once before bed which kept it really clean in there. I made sure she had food and water always and everything and I also took the kits out of the box and have took the box. Right now their cage is up off the ground and they are back out checking it out.