I had an interesting discussion recently with a student involved in the social sciences. This person expressed a feeling of guilt due to not having followed a biblical practice. While some biblical practices are possibly matters of debate, this one was not controversial. We'll suggest it had to do with deciding to study what the Bible says so as to know what God desires. The person talking to me brought up a different issue, but one which was similarly uncontroversial.
The root of the question amounted to this. "How do I deal with a guilty conscience, especially when I know it is guilty with reason?" It's essential to this question that the person I was speaking with agreed that the conscience was correct and that the neglected practice was something the Bible generally assumes will be the norm. How do we deal with a conscience?
First, when our conscience is nagging us about something, we want to explore whether it is right. Christians admit to having a fallen nature which can lead them astray. So we look at a reliable source outside ourselves to evaluate our conscience's claim.
When we find that our troubled conscience is operating correctly and we are rightly guilty, there are effectively two possible responses, one good, and one bad.
On the side of the bad response, we can choose to harden our conscience, maybe by minimizing our failure or denying that there is anything actually wrong. This effectively leads to a denial of God and a rejection of all the good he pours out on those who trust him. Such a denial of what we have established as valid guilt is always a terrible move. Don't do it!
So what is the good response? You have neglected that which you should do. Traditionally, theologians call this a "sin of omission." You omitted the good which God showed you was yours to do. 1 John 1:9 tells us to confess that before God and He will forgive us. That is of primary importance. The forgiven conscience is not guilty. However, if you want to avoid future guilt, you also want to try not to omit the practice. Back to our earlier example of feeling guilty for not learning what God says in Scripture. Confess your failure, and start reading and learning what the Scripture does say. Then, as you learn and grow in understanding, you will quickly see your conscience was right. You did need to do the reading. And now you are no longer omitting it.
When your conscience is right, it is a helpful guide!