Ensapa, just want to point out that students of Lama Zopa certainly know of Je Pabonkhapa as several works by him have been translated under Rinpoche's guidance, such as retreat advice and the incredible work entitled Heart Spoon: Encouragement Through Recollecting Impermanence.
Lotsawa David Gonsalez is also providing many excellent translations of works by Je Pabonkhapa.
This discussion about the use of texts by Lamas who considered 'unclean' is an interesting one. While Lama Zopa hasn't overtly criticised or disparaged Pabongka Rinpoche, there are many institutions who have, including sadly, individuals from the great monasteries like Gaden.
So, we would be inclined to ask, does this mean that these institutions would deny all teachings and texts given or composed by lamas such as Pabongka Rinpoche and the lamas who arise from that lineage (Trijang Rinpoche, and all other lamas who have received teachings from him?) The monasteries are removing traces of Pabongka Rinpoche's names, but they would still study Liberation in the Palm of Your Hand - widely known to be be based upon Pabongka's teachings, edited by his heart disciple Trijang Rinpoche!
And what of the texts by Panchen Sonam Dragpa? Still used as central texts by every single monk in Gaden Shartse and Drepung Loseling monks aspiring to obtain their Geshe degrees. While the foundation of all their study is rooted in the texts of Panchen Sonam Dragpa, they are also being forced to deny his incarnations and practice - so what does this mean? Are the teachings holy and correct? Or tainted and harmful? Surely it can't be both. How can we deny the Lamas but continue to study their teachings and hope to gain knowledge, understanding, realization and attainments from them? That is like saying that you hope the water you are drinking from a cup lined with poison is pure, clear and beneficial.