Agressive, stressed and... "Traumatized" Rabbit

My bun, Loaf, is a 3 month old female miniature Dutch. She used to had a very sweet behavior, and didn't mind being picked up. She would always lick my hands.
Then, one day, I had to cut her nails (I've already done it three times), which she absolutely hates it. Lots of stress and trying to hold her still was hard. But nothing new there.
Later on that day, I picked her up to sex her myself for the first time, because I had to make sure she was a female (my boyfriend was going to get him a bun too, and the guys at the pet store I bought Loaf didn't look like they knew what they were doing).
She hated it the most. Lots of stress on trying to hold her still.

The thing is: now she doesn't let me pick her up, keeps running away and, when I finally manage to get her, she makes complaining noises, try REALLY HARD to get away. Once I tried to pick her up and out of her cage, she bited me. Now: NONE of these things never happened before. She's not hurt, Because she's running and doing all of her stuff normally. I even tried to show her that I'm not picking up for hurting her or so, by petting her and trying to calm her down. It didn't work. These have been happening for 4 days now.


Now, I realize it was a mistake making her go under two stressful situations in the same day, but how can I fix it? Please help me, I can't stand chasing her every time I have to put her in her cage.
Thank you very much
(Please pardon any mistakes, english ain't my native language)

I'm not 100% sure, but it sounds like it might have just been timing. Regardless of gender, your bunny is probably getting hormonal about now. So, she (or he) is getting more easily frustrated and having some personality changes. You just happened to do these things at the same time this was starting.
As for your English, you are better than most native speakers. I would not have known it was not your first language had you not said something. Actually, I am going to school online to be an elementary teacher. You write better than many of my classmates, and these are people who want to teach.

It could be a combination of the factors of the stress and the hormones, however to me it mostly sounds like she's scared. Take everything slowly, calmly and quietly. Don't chase her around to put her back in her cage. Is her cage at floor level? If so, encourage her in with her absolute favourite treat. I find if Bandit is running from me, the best thing to do is lay down on my belly and slowly approach that way, reach out with a hand and rub the head and move on to picking her up from there. It may take a little bit of time for her to trust you again, but it will come back again

I also suggest approaching her to pat her, and give her a treat, but don't pick her up and then distance yourself from her again. This way, she won't always associate you approaching with getting picked up.