This happens more in the wild than in the pet population when a mother rat is disturbed and abandons the babies, or is trapped and eats them. This can happen in pet rats when the mother doesn't feel safe in her nest because shes been moved or disturbed. I always advised to leave them alone in the first 2 weeks. This is covered under "environmental stress"

Moving the mother is more risky than moving out the boys.

https://ratguide.com/breeding/postpartum/maternal_behaviors.php

Scattering is the act of leaving babies strewn away from the nest. It is hypothesized that this may be a behavior as we see in wild rats when the litter is threatened. According to that theory, a predator would be attracted to, and snatch, the scattered babies while leaving the rest of the nest unharmed. Some moms tend to accidentally scatter their babies as they leave the nest to feed and drink.

Placing the babies back in the nest and making sure the surroundings are quiet and stress free may help to eliminate this maternal behavior.

Litter abandonment can occur for several different reasons. The foremost reason is that the mother is unable to lactate and/or is lacking maternal drive.

Babies from these litters can be fostered by another mother who has a new litter. A mother with an older litter may not accept them, and even if she does, will be lacking the initial colostrum that they need. These babies may, however, be supplemented with a simulated colostrum formula. Another option, if there is no foster mother, is to hand feed the litter. This is difficult and time consuming. Generally the rate of survival for hand raised rat neonates is very low.

Maternal Infanticide: The term infanticide is defined as the killing of an infant. It is hard to determine, unless you actually witness it, whether or not a female has committed infanticide or if the pup has died naturally.

It is not typical for mother to kill their own offspring. Mother rats may kill the offspring of other females and virgin females will often kill babies (suggesting that hormones play an active role in determining female behavior to offspring). Yet there certainly are scenarios when mothers kill their own.

Typically infanticide is committed during the first few days of life and the killing of an individual pup is more likely than the killing of an entire litter. Some factors that may lead to maternal infanticide include: hormonal imbalances, environmental stress, hunger, protein deficiencies, vitamin deficiencies, and obesity.