There is a debate in the Gemara (Gitting 19) and Rishonim (Medieval Halachic scholars) concerning the case of "Ketab Al Gabeh Ketab" – where a scribe adds a second layer of ink onto the letters in the Tefillin or Mezuza. If a scribe sees that the ink is beginning to fade, and so he goes over the script with an additional layer of ink, which layer is considered the primary script? One view maintains that since there was nothing before the first layer of ink was applied, the "Ketab Tahton" ("lower writing") is considered the primary script of the Tefillin or the Mezuza. The lower script is, after all, the one which transformed blank parchment into a script, and thus it is deemed primary even after it is darkened. The second view, however, argues that when a person looks at the parchment, he sees the upper layer (the "Ketab Elyon"), not the lower layer. As such, the upper layer should be considered the main script of the Tefillin or Mezuza.
Halacha follows the first view, that the original layer of ink is considered the primary script. One practical application of this principle involves a case where only part of the text has begun to fade, and the Sofer wants to darken the letters in question. As we know, the text of the Tefillin and Mezuza must be written in its proper sequence. Thus, if we would view the upper layer as the primary script, darkening certain letters would invalidate the Tefillin or Mezuza, because those letters would be viewed as having been written now, when they are darkened, and the text is thus written out of order. But since Halacha follows the view that "Ketab Tahton Ikar" – the lower layer is the primary script – faded letters may be darkened, as long as they have not completed faded and are still recognizable by a child.
Another application of this rule has to do with the writing of G-d’s Name in Tefillin and Mezuzot. The Shulhan Aruch (Orah Haim 32) writes that before writing Hashem’s Name, the scribe must verbally declare and have in mind that he writes the Name "Le’Shem Kedushat Ha’Shem" – "For the sake of the sanctity of the Name." If he writes a Name of G-d in the Tefillin or Mezuza without the proper intent, he cannot simply write it again over the original layer of ink with the required intent. Since the bottom layer of ink is regarded as the primary script, adding a second layer will not help in rendering the writing valid. Of course, the Sofer cannot erase the Name, and thus he is faced with a Halachic dilemma which the Poskim address. For our purposes here, however, the point is that he cannot write over the Name, because the original layer will still be regarded as the main script, and the parchment is thus invalid.
Summary: If some letters of the Tefillin or Mezuza are faded, the Sofer can add a layer of ink to darken them, as long as they have not faded entirely and are still recognizable by a child. If a Sofer wrote the Name of Hashem in Tefillin or a Mezuza without the required intent, he may not write over it with an additional layer of ink with the proper intent.
