Well, this is something I haven't heard before and I find the comparison to the Shugden issue quite a strange one. I have been intrigued by the recent discussions about Kopan / FPMT / Lama Zopa with regards to their practice of Shugden so have been doing some reading on the Lama Yeshe Wisdom Archives. I found this:
At one point, when things in Tibet became very difficult politically, His Holiness came to Dromo Geshe Rinpoche’s monastery in southern Tibet. At that time the Tibetan government could not decide whether His Holiness should go on to India or back to Lhasa. So His Holiness and his ministers consulted Dromo Geshe Rinpoche’s monastery’s protector, the one in question. Through the oracle, Shugden said that His Holiness should not go to India. This protected Tibet for another year or for so. What I have heard is that after that experience, His Holiness would recite prayers to Shugden regularly. However, after many years of analysis, when His Holiness was about to take the initiation of Shugden, he received signs in a dream that he should not. As a result, he didn’t take the initiation.
This is the same as what Guru Shakyamuni Buddha did. He first became enlightened inconceivably long ago, not, as history tells us, two-and-a-half thousand years ago in India. According to the Theravada tradition, that’s what happened, but the Mahayana does not accept this—we believe he became enlightened inconceivably long ago. Therefore, as an enlightened being, how can the Buddha make a mistake? He simply practiced Hinduism to show sentient beings that it was the wrong path. This is just what His Holiness did; he practiced Shugden to show us it was wrong.
The blinding difference, I'm sure you'll all note however, is that when Buddha decided not to pursue the path of Hinduism, there was no forced voting, persecution, ostracism or burning of Hindu statues. And that's just the tip of the iceberg.
Just wondering what your thoughts may be on this?