How can one deal with the custody of three children after separation, taking into account the difficulty of the matter for the wife and her intense love for her husband?

There is a difference of opinion among scholars regarding this matter. Some scholars are of the view that committing zina (fornication/adultery) with the mother prohibits her daughter from the adulterer. This is the view of Abu Hanifa, An-Nawawi, Ahmad, and some Malikis. Others are of the view that zina does not result in any prohibition whatsoever. This is the view of Ash-Shafi'i and Malik. The reason for this difference of opinion goes back to the interpretation of the meaning of "nikah (definition)" (marriage/sexual intercourse) linguistically or jurisprudentially. A fatwa (definition) (religious edict) was previously issued for prohibition as a preventative measure and to sever ties, especially in this era where deterrents of faith have weakened. Nevertheless, the opinion of non-prohibition is strong due to the lack of conclusive evidence that prohibits the daughter of a woman with whom one committed zina, and the basic principle is permissibility. If it is established that the matter is one of scholarly dispute, and that the opinion of non-prohibition is equivalent to the opinion of prohibition, and your continuation with your wife will not lead you back to your previous state, then hold on to your wife and fear Allah the Almighty.