And the reason of this is also as evident as is the experience of it because conscience remains in part defiled in a man that is regenerate; and though we are sprinkled from an evil conscience in part, yet not wholly: so as though our persons are fully discharged from the guilt of our sins, through the sprinkling of Christ's blood, before God; yet the sprinkling of that blood upon our consciences, whereby we apprehend this, is imperfect.
And the reason is, because this very sprinkling of conscience, whereby it testifies the sprinkling of Christ's blood, and our justification thereby, is but part of the sanctification of conscience, as it is a faculty, whose office and duty is to testify and witness our estates; and therefore, as the sanctification of all other faculties is imperfect, so of conscience also herein. And hence it is that when God's Spirit forbeareth to witness with conscience the goodess of our estates, and ceaseth to embolden and encourage conscience by his presence, and the sprinkling of Christ's blood upon it against the remaining defilement, that then our consciences are as apt to fall into fears, and doubts, and self-condemnings, even as much as when be withdraws the assistance of his grace, those other faculties are to fall into any other sin. And therefore, as the law of sin in the other members may be up in arms and prevail so far as to lead us captive unto sin; so may the guilt of sin in our conscience remaining in part defiled, by the same reason prevail against us, and get the upper hand, and lead us captive to fears and doubting; and cast us into bondage.
From A child of light walking in darkness