Does my saying, "O Lord, why are You doing this to me?" then my adding, "out of a desire for knowledge, not out of objection," nullify my deeds or cast me out of the fold of Islam?

We advise you to avoid obsessive thoughts (waswasah), and you have not departed from Islam. When a Muslim is afflicted by worry or distress, they should draw closer to Allah Almighty through supplication and acts of worship. Among the well-known supplications in times of distress are: "Allah, Allah is my Lord, I associate nothing with Him," and "O Allah, I am Your servant, son of Your servant, son of Your female servant...," and "O Allah, Your mercy I hope for, so do not leave me to myself for the blink of an eye...," and "There is no god but Allah, the Almighty, the Forbearing; there is no god but Allah, Lord of the heavens and the earth, and Lord of the Magnificent Throne."