Hey there!  Kudos on rescuing them from being raised for meat (ew as well!), were always happy to hear that buns were rescued from being eaten. 

Typically the number one suggestion to help bond with bunnies is sitting down (or laying down, like i did!) with your buns and getting on their level. It’s less intimidating to them, and kind of gets them used to your presence. So i suggest putting them down in a closed in area, big enough for them to have some space to run around, and sit down in the area with them. Do this for about an hour a day, whenever you can or for however long you can, it doesn’t have to be an hour either, and completely ignore them. It helps teach them that you won’t mess with them all the time, and that they’re safe around you. 

Its the best technique to get them used to you, and if they approach you don’t touch them or pick them up for the first couple sessions. After a few sessions, you’ll notice a difference in your female rabbit guaranteed! 

Rabbits are very territorial, and sticking hands in their cage is invading their territory to them. So the thumping is from annoyance/irritation. It happens whenever i put my bunny on the ground after giving him a brushing or giving him medicine. He gives a little thump to let me know he isn’t happy. Its normal. 

I did this with a bonded pair i have (male x female) and they now let me pet them and the female even approaches me for pets now. Probably hoping for vegetables, lol! Where as before, they were stand offish and skittish. They didn’t want to be touched or bothered.

You can also try offering your hand to the female, like put your hand up to her nose. If she bows her head, give her a quick pet on her head but then take your hand away right after the quick pet. If she runs away, don’t follow her and leave her alone for a minute or two. Then offer your hand to her again.  I suggest doing this while they are running around inside a pen or just a closed off area, but not in their cage as your female seems to not like that! 

This lets her know that you won’t pick her up, or mess with her, if she doesn’t want to be bothered. It really helped with my male rescue bunny, who hated being bothered/touched. Now he bows his head all the time and wants to be snuggled! 

Good luck, and keep us updated!