There are still many statues within the monastery that still has DS's mantras inserted into. Perhaps, even the main statue of Tsongkhapa in Ganden has Dorje Shugden's mantras inserted inside as they are actually the one and the same in reality. Does this mean that everyone is still praying to Dorje Shugden in reality? So why did the Dalai Lama not inspect those statues that were consecrated by none other than Trijang Rinpoche, or high Lamas that were also for sure, Dorje Shugden practitioners? If they were, it is without a doubt that those statues were inserted with Dorje Shugden mantras. In one way or another, they were praying to Dorje Shugden all along even if the main statue was not present. And they still are till this very day. If the Dalai Lama really wanted to remove everything, he would have to need to replace the statues as well as they also contain Dorje Shugden images inside them as well. But they remained untouched.
on what Zach had said about the Nyingma termas, not every single terma is not authentic. Termas whose teachings can be traced back to a source is considered authentic. If not, why would there be a Dorje Shugden Terma that is in existence? I believe that Lama Tsongkhapa also had Nyingma Gurus as he sought teachings from all traditions of his time, so it does not mean that it is not possible to work out the differences between Nyingma and Gelug and have them assimilated together. After all, Guru Rinpoche is also Tsongkhapa and they are of the same mindstream and we should not say that one tradition is better than the other.