What is the reason for doubts in religion and faith and the loss of certainty after ceasing to commune with Allah, and is this related to sins, envy, or the whispers of Satan, and how can one get rid of these thoughts and draw closer to Allah?

These thoughts are whispers from Satan, aiming to prevent you from doing good. You must strive against them and repel them, for they will not harm you as long as you dislike them. They will depart from you through struggle, so continue to supplicate to Allah, seek refuge in Him, and remember Him. The best remembrance is reading the Quran with contemplation. Avoid sins, both apparent and hidden, and repent from them. Strive earnestly in supplicating to Allah to let you taste the sweetness of faith, and do not grow weary of obedience, even if your feeling of its delight is delayed.