run checkForUnusedStyles() and it will remove all unused styles in your documents

unused_styles.jsx

function checkForUnusedStyles() {
    var currDoc = app.activeDocument;
    var myParStyles = currDoc.paragraphStyles;
    for (i = myParStyles.length-1; i >= 2; i-- ){
        removeUnusedStyle('paragraph',myParStyles[i])
    }

    var myCharStyles = currDoc.characterStyles;
    for (i = myCharStyles.length-1; i >= 2; i-- ){
        removeUnusedStyle('character',myCharStyles[i])
    }
}

function removeUnusedStyle(styleType,myStyle) {
    //clear find change settings    
    app.findTextPreferences = null;
    app.changeTextPreferences = null;

    if (styleType == 'paragraph') {
        app.findTextPreferences.appliedParagraphStyle = myStyle;
    } else {
        app.findTextPreferences.appliedCharacterStyle = myStyle;
    }

    var myFoundStyles = currDoc.findText();

    if (myFoundStyles == 0) {
        myStyle.remove();
    }

    //reset find change settings
    app.findTextPreferences = null;
    app.changeTextPreferences = null;
}