I suspect it is to do with not wanting to be separated or just “put away” if they’ve been getting more space due to the bonding. He’s probably found this is an effective way to communicate with you. If he growled and you let him be, he would have learnt this gets results so he could keep using it. Jersey is quite vocal like that. I just do what I need to then spend some time petting her and “making up”. lol
Maybe you could try herding him in or herding him into a carrier then taking that to the pen. So avoiding picking him up. Just so it doesn’t develop in his mind that when you do pick him up – it’s going to result in something he doesn’t want. You could reserve the times you pick him up for more positive interactions. Have you been able to do that in the past – just pick him up for a cuddle that he enjoys to?
Do you have a pen you can make as a night enclosure for them both? I know you mentioned concerns with Wooly about the levels in Leopolds condo. Could you block them off somehow and just allow them the lowerer area perhaps?
I’m afraid you are going to feel on the outer with them newly bonded… they might have a bit of an Us (rabbits) and Them (humans) mentality going on but I think after a while you can start to re-establish your relationship with them.