What is the Quranic solution to the suspicion of women being raped, especially what happened to Muslim women in Bosnia, and the ensuing questions about God’s protection of them, and the future of their children and their lineage?

If you believe that nothing emanates from Allah's knowledge and wisdom in vain, and that He is just and wrongs no one, and you work to repel the thoughts you are referring to, then they will not harm you. Rather, they are from the cunning and whisperings of Satan. The rape of women is an injustice and a trial from Allah. If the wronged woman shows patience, it will be better for her in this world and the Hereafter. The ruling concerning the child of a raped woman is the same as the ruling concerning the child of adultery: he is attributed to his mother and not to the fornicator.