What is the ruling on a civil marriage that took place between a Muslim man and a non-Muslim woman, after which she embraced Islam, and they had children whom they raised well, knowing that no legitimate religious contract was concluded until years after the civil marriage, and is this considered adultery?

Congratulate your sister on her embracing Islam, and encourage her to remain steadfast and to raise her children upon the values of Islam. The lack of official documentation for a marriage does not affect its validity, as documents are for safeguarding rights and resolving disputes. Trials may not be a punishment, but rather a sign of Allah's love and a means of elevating one's status. Allah may test His servants to expiate their sins or to raise their ranks.

One must disregard whispers (waswas (definition)) and focus on blessings, and strive in prayer and drawing closer to Allah. For the believer, all of his affairs are good: if he is afflicted with adversity, he perseveres, and if he is granted ease, he gives thanks.