I am in the process of working on a commentary on the Pastorals and the Johannine Epistles both in one volume. While dealing with the latter I was looking at 1 Jn. 3.19-20 today -- "This is how we know that we belong to the truth, and how we set our hearts at rest in his presence, whenever our hearts condemn us. For God is greater than our hearts, and God knows everything."
I came across a wonderful passage in a commentary by William Loader on the Johannine Epistles (pp. 43-44) on this text where he stresses that the writer of 1 John....
"assumes conscience [or heart] may deceive in much the same way as feelings may deceive. Faith means trusting in God’s love and making ourselves available for its action despite what we may feel. Faith cannot be based on feelings. Nor should its criterion of authenticity be absence of struggle. A troubled conscience or mind may coexist with a life of faith. By shifting the basis for confidence from human feelings and inner harmony to hard faith facts about God and behaviour, the author is boycotting a common religious trend, then and now, to make inner human experiences the criteria of spirituality…. It would [also] be wrong to read this passage as devaluing conscience or our thoughts and feelings altogether. They may be a guide, but their quality as guide will be determined by the quality of person who is being guided. The author is not operating with an idealistic notion of conscience as somehow representing the voice of God within….He operates rather with the notion that our thoughts and feelings are part of our own system of awareness which may be misinformed and misguided. There is also a touch of realism in the author’s obvious appreciation that Christians may well at times have to struggle with unresolved tensions within their personalities which have their origin somewhere other than God. There is a profound comfort in the assurance that God is greater than our conscience and knows all (3.20), because this God is the God of love and compassion and may be trusted."
This passage has many insights to be contemplated but I will share just three: 1) a troubled conscience may at times be a good thing (a sign that one is deeply concerned about an injustice), it may at times be a bad thing (a sign of something done wrong), but it is not an infallible thing. The Bible never suggests--- "let your conscience be your guide" or "to your own heart be true". The problem with this sort of advice is that our hearts or minds or consciences are just as fallen and prone to error as our feelings. 2) There are times when persons struggle with being sure they are Christians. They wrestle with feelings of not being good enough, and the like. This text should be a great comfort. God has the trump card--- he can over-rule your feelings or tender conscience and reassure you that you are in right relationship with God even if it does not feel that way; 3)the quality of the conscience depends on the character of the person in whom it resides, and just how sanctified that person truly is. Sometimes mass murderers sleep just fine at night, with no qualms of conscience. Sometimes some Christians have a weak conscience, and find offense in any little thing. Notice how Paul says that the overly scrupulous person in 1 Cor. 8-10 is the Christian who is weak in faith. In either case the conscience is not a good barometer of the truth or what is right. This is why at the end of the day the author of 1 John stresses that we must trust God and place our trust in the Gospel message, not trust ourselves as the last arbiters of truth, right, "and the godly way" and finally 4) the Pauline rule, whatever is not of faith, is sin for you, is a good one, when one is wrestling with one's conscience. As faulty as the conscience may be, it is sometimes a good nagging voice that approves or disapproves what you are contemplating doing. You should listen to the voice, but not give it the final say. That belongs to God and God's Word.