These controversies served to divert his efforts even further away from his main objective - the project to build a collection of Portuguese diplomatic documents from the founding of the monarchy to the 19th century. In fact, this was a project that became official in 1824 and again in 1842 in the reigns of D. João VI and D. Maria II.

In spite of all this, Santarém still managed to publish eleven volumes of the Quadro Elementar... by 1853. Those that were edited posthumously (seven between 1858 and 1876) by Rebelo da Silva and Mendes Leal, under the auspices of the Academy of Sciences, underwent a change in their purpose and suffered chronological amputation (from 1501 onwards) which moved them irretrievably away from the initial project. The same happened with Corpo Diplomático... (The Portuguese Diplomatic Corps...), a title used by the same institution for similar ends, which Herculano and his followers wished to include in the national historiography from the 1850s on: that is, documental exclusivism of Portugaliae Monumenta Historica up to the end of the 15th century and publication of sources to use in anti-Ultramontanism disputes (such as those of the Padroado do Oriente [Portuguese Patronage of the East], the 1857 Concordat and that of the Sisters of Charity).

A veil of silence fell over Santarém’s work after his death in 1856. Only as a result of the actions of his nephew, the 3rd Viscount (1878-1971), in the first third of the 20th century were his writings and correspondence organised and re-edited. The decisive intervention of the historian in the 19th century controversy over the priority of the Portuguese discoveries, glorified under the Estado Novo because of the Infante D. Henrique and the Crónica da Guiné (Chronicle of Guinea), was critically defended by Joaquim Bensaúde and Armando Cortesão but, however, it was downplayed by Vitorino Magalhães Godinho in texts dating from 1943 and 1962. Only with the re-edition of the Atlas and certain selected works (with prefaces by Martim de Albuquerque) in 1989 and publication of works by Sérgio Campos Matos in 1998 that contextualised and problematised the issue, did the multidisciplinary and critical work of this historian, geographer and map historian, praised by such impartial contemporaries as Guizot, Humboldt and Navarrete, once again merit the attention of the academic community (on this subject, see Daniel Estudante Protásio, 2009, pp. 256-313).

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