The founder of the Gelug tradition, Lama Je Tsongkhapa, had two main disciples:
- Gyaltsab Je and
- Khedrup Je
While Khedrup Je was the 1st Panchen Lama, Gedhun Choekyi Nyima was recognized, by H.H. the Dalaï-Lama, as the 11th Panchen Lama. He was also recognized as such by the Chinese government that decided to have a say in the so-called “Tulku system [of recognition]”.
Although Gyaltsab Je was the Spiritual Leader of the Gelug tradition (Ganden Tripa) after Tsongkhapa, Khedup Je also became the Ganden Tripa in time, after Gyaltsab Je's passing.
As a result, their philosophical work is highly regarded by Gelug teachers and students. Gelug students still study the 1st Panchen Lama's commenteries, along with Gyaltsab Je's.
Khedrup Je was also a teacher of Gendün Druppa, the 1st Dalaï-Lama. From the time of the 5th Dalaï-Lama, the Dalaï-Lama & the Panchen Lama held the responsibility of recognizing one another['s reincarnation].
It is believed that Khedrup Je was a reincarnation of Subhuti (the one depicted in the Vajra Cutter Sutra, a disciple of Shakyamuni Buddha).
Whether his imprisonment affected the Buddhist community, and if so, in what way, is difficult to tell. His imprisonment means:
… a teacher of H.H. the Dalaï-Lama being imprisoned
… a candidate to the regency of H.H. the Dalaï-Lama being imprisoned
… one of the main disciples of the founder of the Geluk tradition being imprisoned
… a candidate to the position of Ganden Tripa being imprisoned
… a potentially influential of textual commentaries being imprisoned
Most Tibetans still mourn him. If you go to McLeod Ganj or Boudhanath, you will see plenty of posters with his pictures, and printed characters such as “Give back the Panchen Lama!”
Kyabje Lama Zopa Rinpoche (that many think of as clairvoyant, or even enlightened and thus omniscient) said that Gedhun Choekyi Nyima (from whom we have never heard of again otherwise) is still alive, safe and sound.