The Modern Forgery Hypothesis

[nablator]

AFAIK the use of diacritics was an innovation by the Church in medieval times.

Not medieval, 16th century, unless you include the abbreviations. Abbreviations are much older, they disappeared progressively during the 16th-18th century and coexisted with the Neo-Latin diacritics a.k.a. accents (acute, grave, circumflex). I don't think that there is any evidence that the use of the accents was started by the Church or by anyone in particular. It is difficult to find explanations about their systematic use. Book publishers had their own rules, they were consistent in any given book but everyone did not follow the same rules AFAIK.

This article lists some of the typical usages (it is far from exhaustive):
Allan H. Gilbert. (1939). Mock Accents in Renaissance and Modern Latin. PMLA, 54(2), 608–610. doi:10.2307/458579

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