A recent article based on ancient Tefillin found in the Qumran caves near the Dead Sea claimed they found Tefillin boxes that were not colored black on the outside. Based on this finding the researchers wished to make a deduction about halacha, namely, that halacha did not originally demand this coloring.
The knockout punch against this claim is that the Essenes were in charge of the Qumran community and not Jews who were loyal to halacha, the so-called Pharisees. On this site we have some videos explaining the difference in the post: History Videos: Titus, Sadducees, Zealots, Essenes, Pharisees & the Sages of Yavneh by Dr. Henry Abramson. If that is not enough to show the Essenes were outside the halachic mainstream you can do a number of google searches about the Essenes.
Rebuttal #2: Maybe the Tefillin found in the Qumran caves did originally have a black color but in the course of 2000 years the dye came off.
Rebuttal #3: In the production of Tefillin, the Tefillin are usually dyed at the end of the production process. Maybe the Tefillin discovered, were Tefillin in the middle of the production process.
Rebuttal #4: Maybe the Essenes had a shortage of the necessary black dye, but would use it if it became available.
Rebuttal #5: From what Rabbi Yosef Karo writes in his Beit Yosef commentary to the Tur (Orach Chaim 32:40) it is not so clear that there was an absolute requirement to have the batim (boxes) of the Tefillin black, just the straps have to be black. In our times however, Rabbi Karo ruled in Shulchan Aruch, it is a mitzva to make the batim (boxes) black too (apparently based on the stricter opinions on this issue).
Rebuttal #6 Rambam in Hilchot Tefillin, Mezuzot and Sefer Torah Chapter 3, Halacha 14 says that one fulfills his requirement even when the batim (boxes) are not black. It is just a beautification of the Tefillin to have the boxes colored black (in contrast to the straps where black is a requirement).
Some Achronim try to make Rabbi Karo’s ruling in the Shulchan Aruch fit with Rambam. I am just presenting the view without deciding that issue.
Rescued Gaza Hostage Begins to Fulfill His Vow to Put on Tefillin Daily
מ ושחורים ואם עשאן מצבע אחר כשרים. בפרק הקומץ (שם) אהא דאמרינן רצועות שחורות הלכה למשה מסיני כתבו התוספות (ד”ה רצועות) יש עושים בתים של תפילין מעור לבן דלא נאמר שחורות אלא ברצועות וכן כתב האגור (סי’ נג) בשם הרשב”א וכן כתב הרא”ש (שם סי’ ח) וכתב עוד מכל מקום נוי תפילין הוא שיהיה הכל שחור ובספר התרומה (סי’ רז) רצועות שחורות הלכה למשה מסיני ושמא גם כן עור הבתים צריך להיות שחור והמרדכי (שם י:) כתב שדקדק ר”י מהגמרא שהקציצה בעינן שחור כמו הרצועות: