Donald Trump did win a second, non‑consecutive term in the 2024 U.S. presidential election and was inaugurated again as president on January 20, 2025, beginning his new administration at that time. (en.wikipedia.org)

Lina Khan’s official FTC biography lists her as former Chair, stating that she served as Chair of the Federal Trade Commission from June 15, 2021 to January 20, 2025. (ftc.gov) Independent biographical information likewise records her term as FTC Chair ending on January 20, 2025, with Andrew N. Ferguson succeeding her; it also notes that while she remained an FTC commissioner briefly until January 31, 2025, she was no longer Chair (the head of the agency) once Trump took office. (en.wikipedia.org)

Because:

• The condition in the prediction (“a second Trump administration beginning in January 2025”) did occur, and
• From the start of that administration onward, Lina Khan was not serving as Chair (i.e., not “running that agency”),

the prediction that she would not be running the FTC in a second Trump administration was borne out by events.