In 1985, he founded the Master’s Degree in Palaeography and Diplomatics at the School of Arts and Humanitiesof Lisbon, with postgraduate seminars in Portuguese Palaeography, Diplomatics, Historical Portuguese Linguistics and Codicology. The course ran until 1994, reopening in 2003 under the direction of B. Sá-Nogueira and with the collaboration of Maria Helena da Cruz Coelho and Armando Luís de Carvalho Homem, as well as his disciple Susana Tavares Pedro, who obtained her PhD in 2008.

Borges Nunes participated in the preparatory meetings for the founding of the Portuguese Society for Medieval Studies in 1985 at the Faculdade de Letras da Universidade de Coimbra [School of Arts of the University of Coimbra], collaborating with Luís Adão da Fonseca and José Mattoso. After 1989, his involvement in the life of the Department of History and the School, which had been intense between 1983 and 1988, began to wane.

In 1992, the untimely death of his colleague Manuel Mendes Atanázio, one of the few friends he had made in his academic life, along with the Albuquerque brothers, left him shaken and disillusioned. He devoted his last two years of activity to supervising the final theses of “his” master’s programme with meticulous care and attention. He continued his scientific work, mainly in the journal “Brotéria”, with paleographic expertise on Columbian themes - “Mais uma assinatura falsa de Cristóvão Colombo” [Another false signature of Christopher Columbus] and “Uma leitura mais ‘verdadeira’ do criptograma colombino” [A more ‘true’ reading of the Columbian cryptogram] (Brotéria, Oct-Nov, 1993).

In 1994, his retirement marked his complete and definitive departure from academic life, interrupted only to participate as a scientific advisor on master’s degree juries until December 1996. , November 1996, he agreed to sit on the doctoral juries of his disciples António Ribeiro Guerra and Bernardo de Sá Nogueira. These were his final steps in academia.

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