What is the religious ruling on my sister staying with a husband whose flaws became apparent after the marriage contract, given her attachment to him and the fact that my father is only aware of some of these flaws?

If what is meant by "writing the book" is the legitimate marriage contract, then the sister has become a legitimate wife, and the contract cannot be annulled except in the presence of specific defects that entitle the wife to annulment, which are: insanity, leprosy, vitiligo, impotence, or castration. The husband should be advised and reminded of Allah if the defects relate to religion or morals.