Should I leave nesting boxes in the rabbits cage all the time?

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I don't like holding them by the scruff of their neck either but sometimes it's the best way to get them to submit to being picked up. You have to grip quite a lot of skin so they're held very securely. They should calm down immediately, just like a kitten does when it's mom picks it up by the back of it's neck. If I think the rabbit is going to be nervous, or say if a dog comes running up, I will lay my hand on the back of their neck just in case. That way, if they do react, I'm ready. You can usually tell ahead of time because they'll tense up.
I also meant to ask, picking them up by the scruff won’t suffocate them right? I know my mom used to warn me against holding our large orange cat that way because she said the cat was too heavy to hold that way. I feel like my rabbits are close to being as heavy as that cat so I just wanted to make sure it wouldn’t hurt them.
 
The reflex to go limp disappears sometime around 4 weeks old when they are mobile enough (dogs & cats), rabbits don't have the reflex, because a doe cannot pick up kits that way.
Other than that, there are connective tissues going from skin to underlying layers of muscle and such, those are not designed to carry that much weight in an adult animal. You can do damage and hurt an animal that way, giving them reason to fight and panic. Scruffing to keep an animal flat on a table is another matter. I pick them up just in front of the hips if i need a one handed grip, then you have a grip around the spine and way more structure to hold then just skin. And even then only untill i have them close and on my arm or into a transportcrate. Yes, that is way easier with an animal that maxes out at about 4 pounds.
 
I also meant to ask, picking them up by the scruff won’t suffocate them right? I know my mom used to warn me against holding our large orange cat that way because she said the cat was too heavy to hold that way. I feel like my rabbits are close to being as heavy as that cat so I just wanted to make sure it wouldn’t hurt them.
I try everything else first rather than scruffing them. While I've never heard that it will suffocate them, picking a rabbit up by the scruff, especially a larger/adult one, separates the skin from the muscle beneath. 🥺 Unlike cats, rabbits never pick up their babies by the scruff, and their bodies are not built to withstand it (and if anything would make them feel like a predator had them, it would be that!). I have seen the damage when butchering and don't want to have any part in that.

Only very rarely do I grab rabbits by the scruff, but sometimes you're not left much choice. (I like my rabbits, but I am not willing to sacrifice my own skin for them!) In those incorrigible cases, I collect both ears and scruff in my right hand, but I do NOT lift or carry a rabbit that way. Once their ears and shoulders are immobilized, they tend to stay still, though I would not call it relaxed. When I have them immobilized, I reach under them and lift them, by the body, with my left hand. Sometimes my hand is under their belly, sometimes it's cupped under their hindquarters - this depends on how big the rabbit is.

I don't carry them that way, either, since they tend to start flailing if you have very far to go. What I normally do is pull them up against my own body and carry them that way (my rabbits are gentle, even when they're being pills about being taken out of their cages). But I also handle a lot of other people's rabbits which are not gentle, and if I'm afraid a rabbit will bite me, I flip it over on its back in the cradle of my elbow and carry it that way. I've had nasty angry does furiously chewing on their own dewlap in that position, but they couldn't get to me. :ROFLMAO: Once you get where you're going, you just roll the rabbit forward onto the table/ground/whatever.

If you're moving rabbits from one cage to the other, or out to a pen in the yard, and you have trouble keeping them in your arms for the trip, you might consider just bringing a small carrier or even a cardboard box to the cage, pulling the rabbit from its cage directly into the carrier, then carrying them in that. That's what I have smaller kids do with very large rabbits.
 
I also meant to ask, picking them up by the scruff won’t suffocate them right? I know my mom used to warn me against holding our large orange cat that way because she said the cat was too heavy to hold that way. I feel like my rabbits are close to being as heavy as that cat so I just wanted to make sure it wouldn’t hurt them.
I had written a nice long clarifying answer & my ancient tablet froze up & lost it.

@Alaska Satin did a good job explaining pretty much what I was going to say.

My rabbits are 10-14 lbs. I don't have to pick them up by the scruff very often, but my buck was being really rotten the other day (not that I blame him, he didn't want to go back in the cage after being in the playyard) Anyway, I picked held him by the scruff & looked him in the eye & told him to behave. Probably 5-10 seconds. He settled down.

I do have 3 cages that open from the top. When I have to pick up a rabbit from there
1) I talk to them - tell them I'm going to pick them up, pet them & calm them down & tell them how wonderful they are LOL I actually think this is the most important part - talking to them
2) I hold the scruff, very firmly with as much skin as I can get & I put my other hand under their chest.
3) I lift them with as much of the chest as possible, but if they're kicking, sometimes you just have to use the scruff until you can get them to a point that you can get them safely
4) Then I hold them mostly under their chest, but keep my hand on their neck, if they fuss, I tighten the grip on the skin of their neck
5) Also, when they fuss, I say tchhhh tchhhhh at them. I don't think it matters what noise you make, but that sound works for mine and they stop. I think you could make just about any scolding sound.

If they get used to you talking to them, I think it helps & they understand what you're saying. My husband does most of the feeding, but he doesn't talk much. They like it when I come out and chatter to them & sing, they seem to like the singing LOL

They may not have the reflex to go limp I have found that they stop fussing & settle down when I do it.

But I do think you ought to get those arm things & you might be calmer. Or at least less scarred LOL
 
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