We had a similar problem - we'd had Skunk and Fudge for about a month when they'd been in the run for a while and Skunk completely turned on Fudge. It was completely out of character for him as Fudge had been the larger and dominant one of the pair. I'm not sure if they were being territorial about the little cardboard house I gave them or that Skunk just wanted to be the dominant one.
When we put them back into their cage, the chattering and fighting just didn't stop - they never drew blood but they couldn't be around each other and poor Fudge was scared to come out of his house when Skunk was about, or Skunk would try to steal his house. We put Skunk in another cage for 3-4 days near to Fudge where they were both fine, but would chatter if they saw each other.
I decided to try and re-introduce them, and leaving a bath as the last option (well, without putting them in seperate cages indefinitely), I decided to try and scrub down the main cage to get rid of any smells. We put them in their run in the living room at exactly the same time and they did chatter a bit. When I turned on the hoover to clean the sawdust up, they both ran to each other trying to hide from the hoover - after that, they've been completely fine! I really think they rebonded over the hatred of the hoover so it's really funny what SRH said!
They've been fine ever since; some strutting from Skunk, but no real chattering for a while now. They did chatter when I tried to reintroduce the cardboard house back into the run for floortime, the chattering started again so I quickly took it out. I think they were both trying to claim the house for their own. We've now also given them 2 food bowls rather than the one, and everything we buy, we buy 2 of - like the Chubes for example.