Odds are he applied for an exception/appeal.

https://registrar.byu.edu/catalog/2015-2016ucat/GeneralInfo/HonorCode.php

Withdrawn Ecclesiastical Endorsement
A student's endorsement may be withdrawn at any time if the ecclesiastical leader determines that the student is no longer eligible for the endorsement. If an endorsement is withdrawn, no confessional information is exchanged without authorization from the student. Students without a current endorsement are not in good Honor Code standing and must discontinue enrollment. Students who are not in good Honor Code standing are not eligible for graduation, even if they have otherwise completed all necessary coursework. Excommunication, disfellowshipment, or disaffiliation from The Church of Jesus Christ of Latter-day Saints automatically results in the withdrawal of the student's ecclesiastical endorsement and the loss of good Honor Code standing. Disaffiliation is defined for purposes of this policy as removal of an individual's name from the official records of the Church.
The decision to withdraw an ecclesiastical endorsement may be appealed through appropriate ecclesiastical leaders only. As a matter of practice, BYU does not intervene in ecclesiastical matters or endorsements. In unusual circumstances, however, a student may petition the Dean of Students Office to allow an exception to the ecclesiastical endorsement requirement. As part of the petition, a student must (i) complete an Application for Exception to Policy (this form may be obtained from the Dean of Students Office); (ii) sign a release allowing appropriate university officials to freely communicate with the student's ecclesiastical leaders; (iii) prepare a written statement outlining the reasons why, in light of the student's extenuating circumstances, the university should allow an exception; and (iv) submit the completed application, release, and relevant statements to the Dean of Students Office, 3500 WSC, Brigham Young University, Provo, Utah, 84602 for consideration.
When considering the petition, the Dean of Students will focus not on the merits of the ecclesiastical leader's decision to withdraw the endorsement but instead on whether the student has demonstrated sufficiently compelling grounds to warrant an exception to the university's ecclesiastical endorsement requirement. In addition to speaking with the student's present and former ecclesiastical leaders, the Dean of Students may also choose to personally interview the student, who may further explain the circumstances which might justify an exception to the ecclesiastical endorsement requirement. The student bears the burden of persuasion that he or she should be considered to be in good Honor Code standing, notwithstanding the lack of an ecclesiastical endorsement. The Dean of Student's decision regarding the petition will be reviewed by the Vice President of Student Life if requested by the student. The decision by the Vice President of Student Life is final.