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Only 2 babies (accidental litter)

I am glad your female is doing well and is taken good care of her babies.
As you know or likely read in other posts regarding accidental litters, does can become pregnant again right after giving birth.
Also, because does have a bicornic uterus (Y shaped), they can carry babies in one or both sides of the Y. In rare cases a doe may conceive in on side of the Y, and then conceive in the other side of the Y a couple weeks later. This is rare, and of course impossible since you said you separated them right after he breed her.
If you leave a female baby with mom, baby may bother mom trying to nurse.
It must be difficult to part with adorable babies even when you know they are going to good homes. That is how I went from 3 to 9 bunnies in one day in 1991! Also why my bunnies are fixed (isn't it the opposite?)
 
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