Q. If someone has a pair of tefillin that have some scratches on the batim, which expose a lighter colour underneath, can he use a black marker to touch up the tefillin himself, or is he obligated to take the tefillin to a Sofer for retouching?

A. The ink used for painting Tefilin does not have special requirements and ingredients, as the ink for writing them has. However, due to different issues it is better to avoid using a common black marker

The recommended special ink or paint can usually be acquired in stores that sell Tefilin and sometimes Judaica.

Often, people who wear Tefilin paint themselves the discolored areas, commonly the corners and edges.
But it has to be done with the special intention or kavanah to be ‘Leshem Kedushas Tefilin’ or for the sake of the holiness of the Tefilin, and that is essential. The words should be expressed verbally before applying the ink.
Horav Aharon Miller Shlit’a suggested to take them first time to a Sofer and to ask him if you can watch and learn how it is done.
Rabbi A. Bartfeld as advised by Horav Aharon Miller Shlit’a