Not likely. Unless she has a record with CPS which is REALLY bad, it is not likely that a court would take her children from her and place them with him. Assuming that they are living together, tell her not to move out & leave the children with him, though. She should cause him to move out if she wants their living location (assuming she wants the divorce) and if he does not agree then she can file for divorce with temporary orders granting her exclusive use of the home. (If she does not want to stay there, then she can move out but make sure she takes the children with her. She does not want him to make a claim that she abandoned them.)
Although I have answered the question to try to help you, you should consult with a lawyer in your area in person on the matter. In addition, my answer does not establish an attorney-client relationship between us.