Here is what Thubten Jinpa had to say in 1997 in the forward about the Yellow Book:
...Also included in this volume is the controversial work which later became known as "The Yellow Book". Written as a somewhat stylized literary piece, this work is a faithful recording of events relating to what could be perhaps described as the "oral history" of a particular period of Tibet.
Geshe Thupten Jinpa is the Dalai Lama's personal translator and to be that one has to be a master of the Dharma himself, not to mention, be highly trusted by the Dalai Lama. Wherever the Dalai Lama is, Thupten Jinpa is always close by. It is interesting that even as the Dalai Lama banned Zemey Rinpoche from His Holiness's close circle and literally treated him as persona non grata, it was Thupten Jinpa, the very close disciple of Zemey Rinpoche whom the Dalai Lama kept by his side all the time.
Some thought that perhaps Thupten Jinpa "changed sides" but this is not so because recently he was spotted visiting and make prostrations to the throne of his Guru, the great Zemey Rinpoche. Surprisingly, this must have been known by the Dalai Lama and yet there was no rebuke from His Holiness. Thupten Jinpa remained loyal and devoted to Zemey Rinpoche all these years and witnessed his Guru being ousted and disparaged by the Dalai Lama and yet under instructions from Zemey Rinpoche, he served the Dalai Lama with true loyalty. A lot of things do not make sense to the untrained eye.
Similarly, we see the Dalai Lama banning the practice of Dorje Shugden that was given to His Holiness by his Guru, Kyabje Trijang Rinpoche. Even as the Dalai Lama seemed to have turned against his Guru (as Thupten Jinpa appeared to as well) and even to the point of saying that his Guru was "wrong", Trijang Rinpoche from the start had advised all to keep trusting and supporting the Dalai Lama.
The Buddhas certainly work in mysterious ways.