I know the Byzantine Empire heavily employed eunuchs across its administration and religion in high positions, yet towards the end of the Empire they were more and more marginalized and lost their influence. What caused this loss of power and how was it implemented?
From "The Eunuch in Byzantine History and Society", by Shaun Tougher; Chapter 8 - "The Twilight of the Byzantine Eunuch":
During the period from 1204 to 1261, when Constantinople was lost to the Byzantine empire and regional powers arose in Epirus and at Nicaea, eunuchs are elusive in the historical record. Guilland notes, for instance, that George Akropolites, who wrote a history of the years 1203-1261, does not mention any eunuchs. Even after the recapture of Constantinople by Michael VIII Palaiologos (1259-1282) in 1261, the number of politically important eunuchs found existing in the Palaiologan period is minimal.
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The existence of politically significant eunuchs under the Palaiologoi does indeed seem limited then, but as under the Komnenoi and the Angeloi there is the sente that eunuchs were still a feature of the Byzantine court, and of Byzantine society in general. Although the fourteenth-century treatise of Pseudo-Kodinos detailing civil and ecclesiastical offices and court ceremonies does not single out eunuchs for special attention (unlike the ninth-century Kletorologian of Philotheos), Gaul suggests that this indicates rather their greater integration in Byzantine society: offices were potentially open to them. More concrete evidence for the survival of eunuchs existe.
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Considering the brief overview of eunuchs in the periods 1081-2014 and 1204-1453, it can indeed be asserted that eunuchs did not completely disappear from the Byzantine landscape (at least not until the fifteenth-century) bu that the existence of individual eunuchs who wielded significant political power or influence did decline, the last great example being that of Andronikos Eonopolites. It seems that the thirteenth century does constitute the key turning point, as Guillard asserted. Politically prominent eunuchs may be scarce under the first three rulers of the Komnenian dynasty (especially John II), but there are some, and under Andronikos I and the Angeloi such eunuchs are much in evidence. I is , then, entirely legitimate to inquire why this apparent shif occurred.
I wonder if the reduction in general of the Byzantine state undermined the acquisition of a great number of eunuchs. After all, during the more affluent Ottoman period, eunuchs were quite common.