First off, welcome to the joys of bunny parenthood! It’s perfectly okay to be worried..you’re new to this. Calla Lily is probably just upset because she’s in a new place with new people who are having to give her medicine. Grumpy bunny..lol. After you have finished the pain meds she will probably warm up to you. Continue ignoring them in the floor and she will eventually get curious and come up to you. I would suggest giving her toys and such to cheer her up…some people bond with their stubborn shy rabbits by simply trying to offer hay, pellets or even treats or fruits or veggies by hand. Don’t push it in her face though..simply sit in the floor a good distance away from her with you palm to the floor holding some type of food for a few minutes. If she doesn’t come up to you to sniff and/or eat simply put it near her in the floor, back up and go back to ignoring her. She will associate you with food and understand that you care for her well-being and it might even get her to eat. Also, what kind of pain medicine is it? If it is a pill, I would try to crush the pill and mix it with a banana and syringe feed the banana mixture. Buns usually love love LOVE bananas and she’ll just think she’s getting a treat! If it’s a liquid I guess you could do the same? Just add a couple of slices of mashed banana to the liquid and syringe feed that. Good luck with you buns!

Congratulations on the new members of your family! Once they’re bonded to you, and vice-versa, you’ll never look at other pets the same way again.
Anyway I wouldn’t stress too much about it. Islington absolutely hated my guts for the first month, but then he’s always been the most stubborn rabbit I’ve ever met. He would either huddle and hide, or lunge and try to attack me whenever I was in the room. I tried lying on the floor ignoring him, but even that was not enough to convince my absurdly stubborn bun.
Eventually I tried lying down with food by me, and that finally did the trick. He had hay and pellets, but the tasty leafy greens were always by me. He’d ever so cautiously sneak out, grab a mouthful, and sprint for safety again. Every day I moved the treats just a little closer to me, and in a week he’d sit beaned on the small of my back snoozing while I read.
Just remember patience is key: don’t get discouraged, it’ll be oh so worth it when you win her over!

I would try making them another safe space that’s all theirs. In addition to his cage and enclosure, Islington has a little rug that he has claimed as his own (with much very ponted chin marking). It has some oat groat treats, some apple branches and a little place for him to hide. Whenever I clean his enclosure he sprints to his rug and hangs out there until I’m done.
If that doesn’t work you could always make cage cleaning time a feast time for them. Set up some leafy greens or other snacks they enjoy somewhere outside the cage and let them do their thing while you clean.
I’m so glad they’re beconing more trusting! Just wait until they start begging nonstop, I promise, it’ll happen.

When we first rescue Tully, we had the some issues with him not wanting to come out of his cage. I think it was because he was abandon on a golf coarse. I put a bunch of hidden holes around the room ( we took a bunch of boxes and cut holes in them). Tully started coming out,and exploring. Now he hardly uses them.