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[Tobiaswulf]

My two boys have within the past few days gone from best friends chasing each other playfully to chasing in fear, bounding around off the walls like bullets. I think that one of them may have hit puberty and the other hasn't (they may or may not be from the same litter. Pet stores.) and they have started dominance fighting.
 
The smaller one has been losing fur, assuming it's fur biting from stress. The chasing has gotten him to where he hides in the sand bath where his cagemate can't get to him. The bigger and more dominant one will come up to him, making quiet hoots/coos, like he is lonely, but the bullied one is making angrier noises in response, as if to tell him to get away. He'll leave, and come back again, as if to ask him to come out, and the cycle continues. The smaller one will rarely come out from the dust bath, if only to interact with me or if he knows his cagemate isn't around. It's breaking my heart. They were just fine a few days ago.
 
There's a lot of fur around to clean up, but no physical damage (no bleeding or bites) I can tell to the smaller one. I don't know if I need to separate them, keep them together, separate and try to reintroduce them, or what. The stress is obviously having an affect on the smaller one. His ears are back and he won't splay out comfortably to sleep like he used to. And the bigger one is lonely without him.
 
I've got the two halves of the cage ready to separate them if need be, but I really don't want to have to do it. Is this something they can work out? Do I just wait or will it permanently affect the smaller one's disposition? He's already running to safety every time his cagemate is around and rarely comes out from the bathhouse.

[GrayRodent]

It's going to be a judgement call. Some animals are not compatible with each other and some will settle out their differences. Having a shelter inside the cage is crucial when you have more than one chinchilla. The missing hair is problematic and could be an indicator that something is seriously wrong. Chinchillas are capable of killing each other if they get into a brawl. Perhaps someone who has had an experience like this can comment.
If you separate them it's not going to have permanent consequences. Re-introduction is still possible. If you have separated animals that have lived alone for a couple of years it becomes much more difficult to re-combine them. If you have two males that smell a female in heat (sometimes it can be a female from another species) they can start fighting over that perceived female and they'll act fine once that is over.

[Tobiaswulf]

I've noticed that the fur loss isn't biting, it's pulling. I don't know if it was being pulled out by his cagemate or not or not.

Because he's taken shelter in the sand bath, he hasn't lost any more fur. But strangely enough, at one point yesterday he let his brother in with him, but not again since then. The angry vocalizations have stopped, too, but he's not coming out of the bath for much and still returns quickly when he does. We've been closing the cagemate away into the bottom half periodically and encouraged the bullied one to take the time to eat and drink. He's a lot more lethargic but I don't know if it's because of the stress and therefore lack of sleep or something else.

The cagemate sleeps and chills in the hideaway next to the bath so that he can be close. Right now it's just looking like the bullied one is still afraid he'll get chased again. He's allowed the cagemate close while eating but he spooked and ran back to the bath. I'm afraid he's built a complete distrust even if the cagemate has calmed down.

[kageri]

Can you cage them side by side instead of top and bottom?  They could still see each other, be near each other, but the submissive one would not get chased.  It should rebuild his confidence and hopefully chill out the aggressive one.  Then they can be reintroduced relatively easy.  There is still a chance they would not get along again after being separated but there's a chance they will never get along again if not separated.  Chinchillas can die from stress and it can be really difficult to keep them eating and drinking enough long term if the stress doesn't go away.  Within a couple days of not eating or drinking properly you could have a lifethreatening situation.

[Tobiaswulf]

The cage itself is just separable top and bottom. One of these: http://ecx.images-amazon.com/images/I/51BGznDyXDL.jpg so no.

I'm making sure he's having time without the cagemate for food and water, and after a couple of hours putting the ladder back down to bring them back together.

[kageri]

It's good to have a simple ~3' guinea pig or rabbit cage on hand for emergencies.  You can also use large show rabbit carriers, try bass equipment, or Quality Cage company makes a whole bunch of sizes.  Watch for proper spacing if it has a wire floor.  There is a very good chance something will happen in their lifetime to separate them.  You might even have to move one to another room or be able to cover its cage to reduce stress.  The logistics are a lot more difficult having only vertically attached sections.  Your backup cage doesn't have to be impressive in size and vertical height may even be bad if it ends up as a hospital cage.  It just needs to be versatile and comfortable for temporary use.

[Tobiaswulf]

Any timing/scheduling suggestions for separating them and reacquainting them? And should I seperate them tonight into the top and bottom halves? The second I let the ladder back down, the smaller one retreated back to the bath house and hasn't come back out. I'm worried that he'll be in there all night, bored and sad and stressed and I'm worried about this being a poor quality of life issue at this point, even though his cagemate has stopped chasing him.

[kageri]

I would separate for one to two weeks.  By then whatever got in their system should be gone.  Go by how brave the one is getting.  Then try them in a neutral place to run around.  A dust bath in the area is good for helping them relax and sometimes even bond over a communal bath so long as you are careful to prevent one trapping the other.  We use top opening bath containers.  When they pretty much ignore each other put them in the same cage on a day you can watch them.  Make sure there is more than one house or tunnel of some type.  While they will be used to each others smell and sight they will have to establish a new relationship that fits the changes in their personalities since whatever it was that set them off.  It's not abnormal for things to change between them as they age.  You just hope most events are not big ones.