It is possible you are positioning your pen at angle that seems as if it is losing ink or has a broken tip thus making dull lines. Try using it straight down to see if the ink quality gets better; If it doesn't get better, get a new pen. For the box itself, you should not try to redraw the lines that went dull. For Line extensions, If you are able to realign your ruler to the near exact line extension you made previously, it should be fine to go over it again as long as it's the same color you did before.