The same thing happened to my boys. They weren't raised together. My dwarf lop was 4 years older and he was so placid even before neutering him. He bonded with my then baby Dutch. They weren't housed together as they had a wire mesh in the centre but they played outside together. As soon as my Dutch (Meadow) was old enough to get neutered we took him to the vet.
What I got back was a different bunny. He actually turned aggressive and bit me on a few occasions. I couldn't go any where near his hutch even without him grunting. I honestly, don't know why his behaviour changed all I could think of was that he lost his trust or something had happened to him to him at the vets as before then, he was so laid back. I did a lot of research on his behaviour but that's a different story
First, I had thought that I had to build my trust back with Meadow before re-bonding him with Nuggs. So many times, I tried putting them in neutral ground e.g. the kitchen and as soon as they seen each other they would fight (often Meadow picking fights). It got to a point where I thought it was impossible. I tried swapping toys, putting them in the bath tub, literally every suggestion on the internet.
I continued to let them have their separate exercise area's and they still lived where they could see each other. I think then Meadow was a few years old I decided to try the approach again. I gradually let them see each in the kitchen and they started to groom each other. I continued this for just under a year. Meadow was chilling in the garden and I let Nuggs hop out. Since Meadow was the 'aggressive' one I was a little worried him seeing Nuggs as an intruder and if they started to show aggression (circling each other). My dad was standing next to me to help me if a fight suddenly broke out. Meadow was sprawled out and Nuggs hopped over to him and to my surprise they just lay down next to each other and started grooming, like they did in the kitchen. From that day on, they played in the same run and instead of binkying around they just enjoyed each others company.
Nuggs sadly died a few months ago but Meadow (he's 7 now) has gone back to his normal self with years of building up trust. He doesn't grunt when I touch his bowl or toys or even when I put fresh hay in his tray. He loves to lick my nose. I can now stick my head in his hutch and rest it next to him and I trust him 100%
I hope you find it easier than I did as I had one bully bun on my hands and he's now the most caring, sweet natured boy.
My suggestion is you never rush them and always sit next to them in a neutral room and start stroking their ears so they can then start to groom each other.
It's good that you have separated their cage. I honestly just found my boys preferred their own space, where they could see each other (mesh in the middle of the hutch) and have their own space to get away and just enjoy play time together. Similar to how we have our own bedrooms. Have you parted it with mesh? It will be easier as they still see each other but still have their own space.
So sorry for the waffle I hope I have given you some useful info