It is very common that over the course of time the black ink on a Sefer Torah fades. Although the letters are still fully visible, at times, they are no longer black. Does this affect the validity of the Sefer Torah?
The Hatam Sofer (Teshuvot, Yoreh De’ah 256) rules that even if the ink fades, that is considered to be normal ‘wear and tear’ and the Sefer Torah is still valid. R. Ovadia Yosef agreed, especially in light in the position of the Rambam (Teshuvot 294), who maintains that an invalid Sefer Torah may be read publically. He adds that it is proper to go over the letters and darken them. Regarding Shabbat Zachor, which many view as a Biblical obligation, one should be strict and not read from a Torah with faded letters.
However, this is only true for a Sefer Torah. Regarding Tefillin and Mezuzot, a person should not wear tefillin, or use the mezuzot, until a sofer goes over the letters and darkens them with black ink. He notes that darkening the letters does not violate the principle of "kesidran," i.e., that one must write the parshiot of tefillin in the order in which they appear in the Torah.