[1] In August 2009, Yen joined the disaster relief efforts under the 8th Army Corps following the Typhoon Morakot.

[1][3] He left the post in January 2014, and was appointed the chief of the general staff of the Republic of China Armed Forces.

Further investigation on the host helicopter pilot, Lieutenant-colonel Lau, revealed multiple incidents of corruption and security breaches associated with the 601 Brigade of the ROC Army Aviation and Special Forces Command [zh], which led to 20 officers being either prosecuted or sanctioned.

Yen became the first Chief of the General Staff receiving a demerit in the ROC Armed Forces history.

[16][17] On 3 October 2018, MP Freddy Lim, former Director of the Amnesty International Taiwan, inquired in a hearing session of the Foreign and National Defense Committee in the Legislative Yuan for re-investigation on the Lieyu massacre files in the military archive to render an apology to the victims' families through the Vietnamese Representative Office,[18][19] but Minister Yen disagreed, claiming that troops followed the "SOP" of the Martial Law to execute the orders, and had been court-martialed.