You did the right thing seperating them for a start so well done as if left she could have killed him. Its fairly uncommon for a male and female to fight as they do tend to get on generally but its not unheard of, if it had just been a small fight then i might have put it down to hormones and her maybe not wanting to breed but it sounds like the male had taken quite a beating so wasn't just a one off. How long had they been together and are you positive she is pregnant? Is she displaying any signs she might be? Degus are
social animals so keeping on her own long term isn't the best idea as they can become depressed without the company of other degus but if she proves to too aggressive with others you might have little choice. What i'd suggest doing is waiting for a month or two and see if she has any babies or develops anything that might suggest she is pregnant, just keep an eye on her and give her lots of attention (without handling her just incase shes in pup as could cause her to miscarry) and tickles to make sure shes ok and not getting depressed. Degus are pregnant for around 3 months so you should expect something to happen in the next month or so if she is. If she does have babies then i suggest you keep any females you might have as company for her as she should bond with them and rehome the boys if possible. If she proves not to be then get her a new friend preferably female and introduce them over a period of time and hopefully fingers crossed you should have no problems
Goodluck and please keep us posted
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