I want to have a clear conscience so that I know to judge clearly what is right or wrong.
I want to have a clean conscience, therefore I will not do such an ugly thing.
The dictionary tells that 'clear conscience' is the same as 'clean conscience'. Both are idioms. However, my intuition is that a clear conscience is more about giving a clear judgment, whereas clean conscience is more about avoiding bad deeds and being free of guilt. I might agree that 'clear conscience' covers the two meanings, but I would say 'clean conscience' would better be restricted to the meaning as in the second example. Am I wrong?