Francis Schaeffer in his book, True Spirituality, helps us understand how God cleanses our conscience.
Martin Luther, in his commentary on Galatians, shows a great understanding of the fact that our salvation includes salvation from the bondage of our conscience. It is, of course, natural and right that as we become Christians our consciences should become ever more tender. This is a word of the Holy Spirit. However, I should not be bowed down by my conscience year after year over sins which are past. When my conscience under the Holy Spirit makes me aware of a specific sin, I should at once call that sin sin and bring it consciously under the blood of Christ. Now it is covered, and it is not honoring to the finished work of Jesus Christ to worry about it, as far as my relationship to God is concerned. Indeed, to worry about it is to do despite to the infinite value of the death of the Son of God. My fellowship with God is restored.
Now there may be a price yet to pay for my sins in regard to the state; there may be a harm to individuals that I have to deal with. These things still have to be faced...But as far as my fellowship with the Father is concerned, God says it is restored upon the basis of the value of the blood of Jesus Christ. And if His blood is of such a value as to bring a rebel and a sinner from the kingdom of darkness to the kingdom of God's dear Son at justification, what sin is so black that it cannot cover it?
As I consciously say, "Thank you" to God for a completed work, my conscience should come into rest.
For myself, through the thirty years or so since I began to struggle with this in my own life, I picture my conscience as a big black dog with enormous paws which leaps upon me, threatening to cover me with mud and devour me. But as this conscience of mine jumps upon me, after a specific sin has been dealt with on the basis of Christ's finished work, then I should turn to my conscience and say, in effect, "Down! Be still!" I am to believe God and be quiet, in my practice and experience. My fellowship with God has been supernaturally restored. I am cleansed, ready again to resume the spiritual life, ready again to be used by the Spirit for warfare in the external world. I cannot be ready until I am cleansed; but when I am cleansed, then I am ready. And I may come back for cleansing as many times as I need, on this basis.