Conscience is what we believe about right and wrong. It is not a feeling or emotion. People with OCD often react emotionally to a thought, and the biochemical flaw in their brains makes it "stick" in a way that makes them think that something perfectly innocent may in fact be a sin or be dangerous in some other way. The result is an obsession- an irrational response bearing no relationship to reality that we can't seem to shake.
In our society, we overvalue emotions. We even allow them to guide our decisions and attitudes. Since cognitive psychology tell us that emotions are biochemical responses to thoughts, that might not be as bad a thing for most people as it might be. But for people with OCD, the thoughts are often random and quite crazy. We might even be aware of its craziness if we only examine it. But instead, we listen to the emotion.
If you have OCD, never let your emotions tell you that something is wrong. Instead, identify and examine the thought that produces them in light of God's Word and common sense.. Remember, you conscience is what you rationally think about something, not what you feel about it. And God is not the Author of confusion. When He forbids something, it's something that can be rationally identified. A vague feeling unattached to the violation of an identifiable commandment or law of God is nothing but an obsession. Ignore it.