So after almost two whole years now, I find that I am still having to scoot Mimzy into the crook of my right arm while I take hold (as gently as possible) of the scruff of his neck with the other and use that to steady him as I lift from underneath to get him out of his night pen when it’s time to come out and play.
I hate this practice, but unfortunately it is the only way at present that I can extricate him from the pen safely. And I always massage his neck fur for him after getting him into my lap. I also do not use the neck to fully support him as I lift, it’s just kind of a method I use to keep him from suddenly bolting out of my arms (which he has done before and I never want to have happen again!) He is completely resistant to being gently lifted from beneath, but we are working on it.
Is this bad for him in the long run? I know I am going to have to get his pen on the ground at some point and probably build him and Pip (and hopefully Fiver too someday) a whole enclosure that is floor level and safer and cooler for them than where they are now, but this is a long process. In the meantime, I just want to be sure I am not causing any injury to him in any way.
Ironcially enough, I had to get hold of Fiver one night to clean his heels. I had missed in my attempt to just scoop him out of the pen, and my hand came down on his neck just behind the ears and he seemed to instantly shrink as if this was some sort of submissive behavior he had to display for that kind of touch. (It made me feel awful, btw.) I wonder if it goes back to the momma buns holding them by the scruff as kits? Isn’t this how they carry their (obviously much lighter) babies?
Needless to say, many noserubs and treats later, I finally had clean bunny feet! ^_^ But man I’ll never forget the look on his face. It made me feel sad that maybe someone had daily wrenched him up by the scruff where he used to live. 
I know there are all sorts of ways to safely lift a bunny other than what I’m doing, and I’m trying to get Mimzy to accept at least one of them, but he’s a stubborn bugger. I look forward to getting his cage into an area better adjusted to his finding his own egress without my help…which I think he will be eternally grateful for. >.<