This gets confusing the more I think about it. FPMT have given up Dorje Shugden, but they are also under the guidance of Lama Zopa.
In the FPMT website, Lama Zopa says
"Kopan Monastery had been performing the Dorje Shugden practice from the beginning, as this was Lama Yeshe’s main protector, on whom he relied whenever he needed help for anything. But since His Holiness the Dalai Lama is the one who holds, preserves, and spreads the entire Buddhist Dharma—both the lesser vehicle and the Mahayana, Paramitayana, and Secret Mantra Vajrayana—without the existence of His Holiness, not only Tibetan Mahayana Buddhism but Buddhism in general would suffer in the world. It would be similar to when children are left behind when their parents die. It would be like that.....
....Therefore, it becomes very important to support His Holiness and to fulfill His Holiness’ wishes. For that reason, Kopan Monastery stopped doing this practice. This was done for His Holiness. This does not mean that Pabongka Dechen Nyingpo, His Holiness Trijang Rinpoche, and His Holiness Song Rinpoche have made mistakes. It does not mean they are wrong. Nor does one have to look at the protector as evil. For us ordinary people it is difficult to judge, because we cannot see these lamas ’ minds."
Yet, on the same page:
"Once you have made a Dharma connection with the virtuous friend, your guru, you cannot give up this relationship unless the guru himself or herself says, “Don’t come,” or “Don’t regard me as your guru.” By giving up Geshe Kelsang Gyatso, you have created heavy negative karma in this life. Since you haven’t given me up, I suggest that you confess to Geshe Kelsang Gyatso about what happened, and devote yourself again to this virtuous friend."
Lama Zopa encourages FPMT to follow the Dalai Lama's wishes, which is to give up the practice. But in the 2nd part, he also advises one of his students to "devote himself to Geshe Kelsang Gyatso". How else can the student do that without picking up the practice of Dorje Shugden again? And if he does so, he is going against the 1st part of Lama Zopa's advice. Feels like a no-win situation, either way it is disobeying one of your gurus.
And by making such pronouncements, Lama Zopa is encouraging FPMT to break their samaya with Lama Yeshe and the protector while the 2nd part seems to hint at keeping a secret connection to Dorje Shugden (or is it just wishful thinking!)