Hi,
Our feelings do not always reflect reality. When our conscience bothers us, usually it is reminding us of some choice we made that was sinful and so we feel guilty. But it is also possible for us to have made a sinful choice, and for some reason, we do not feel guilty at all. We need to ask forgiveness for the sinful choices we make because we know that we have offended God whether we feel guilty or not.
When our sins have been forgiven, we know intellectually that they are forgiven even if we still feel guilty. Intellectually we know that our sin is forgiven and so we have to wait for our feelings to catch up with the reality of the situation.
Fr. Vincent Serpa, O.P.