oh crikey! you have more than me!!

The babies should ideally stay with mum until they are 8 weeks, then they can be rehomed and must be seperated. If you want to keep a female with mum it should be fine as long as you neuter them both as they are very hormonal!! You could neuter dad and mum and put them back together once mum is recovered, just becareful because bucks can stay fertile for up to 6 weeks post neutering.

Yes you can clean them out, id pop them somewhere safe with mum whilst you clean the cage out and pop plently of bedding back in, mum will soon organise things, how old are they?

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