And is that grease pencil already part of the rendered video? Or are those grease pencil strokes still in the scene and are editable? You can check your rendered PNG files frames to see if where the line is there’s alpha on it. That way you know that the problem is the rendered video itself. Also if you change the background image to say a red one, is the red color now seen through the lines? You can upload your file if you can with a couple of frames so we can help troubleshoot the problem.
