Lyon's theory is rather flawed.
First of all, the Etymologiae was written in the 7th century. Just because one paragraph from one chapter in the book might possibly be construed as implying a flat earth, does not mean serious scholars for the next 1,000 years all believe the earth to be flat. Without direct evidence of medieval scholars calling the Earth flat, one cannot possibly extrapolate a single book's alleged errors to an entire continent.
The existence of Newton's extremely influential work does not prove 21st century physicists 400 years later are unaware of relativity.
Secondly, it's not clear that Etymologiae actually says the Earth is flat, mistranslation or otherwise. This is what it says:
Orbis a rotunditate circuli dictus, quia sicut rota est; unde brevis etiam rotella orbiculus appellatur. Vndique enim Oceanus circumfluens eius in circulo ambit fines. Divisus est autem trifarie: e quibus una pars Asia, altera Europa, tertia Africa nuncupatur.
The globe (orbis) derives its name from the roundness of the circle, because it resembles a wheel; hence a small wheel is called a ‘small disk’ (orbiculus).1 Indeed, the Ocean that flows around it on all sides encompasses its furthest reaches in a circle. It is divided into three parts, one of which is called Asia, the second Europe, the third Africa.
Barney, Stephen A., et al. The Etymologies of Isidore of Seville. Cambridge University Press, 2006.
Textually, this is ambiguous at most, so the the other argument from proponents of the flat earth myth is the accompanying illustration:
Page from the Etymologiae. Source: Wikipedia
This argument is however easily dismissed. Pick up any atlas or world map today - modern detail and projection are vastly superior, but it's still flat! This is merely the inevitable result of attempting to represent a 3D globe on a 2D surface. It does not mean either mapmaker or the reader actually think the Earth is flat.
Finally, Isidore of Seville left more than just the Etymologiae. In fact, according to the late Italian professor Umberto Eco:
Isidore of Seville (who was surely not a model of scientific precision) calculates at a certain point that the equator was eighty thousand stadii in length.
Eco, Umberto. Serendipities: Language and Lunacy. Columbia University Press, 1998.
This is not particularly accurate, though not that bad considering Christopher Columbus's later example. However, the mere fact that he tried calculate the equator proves that not even Isidore thought the Earth was flat.
Last but not the least, we know for a fact that it is the consensus of medieval scholars that the Earth is indeed spherical.
If we examine the work of even early-medieval writers, particularly in Europe, we find that with few exceptions they held a spherical-earth theory . . . From the seventh to the fourteenth century, every important medieval thinker concerned about the natural world stated more or less explicitly that the world was a globe, and many of them incorporated Ptolemy's astronomy and Aristotle's physics in ttheir work.
Numbers, Ronald L., and Kostas Kampourakis, eds. Newton's Apple and other Myths about Science. Harvard University Press, 2015.
For example, in the 5th century Augustine of Hippo wrote of the antipodes in his hugely influential The City of God that:
[A]lthough it be supposed or scientifically demonstrated that the world is of a round and spherical form, yet it does not follow that the other side of the earth is bare of water; nor even, though it be bare, does it immediately follow that it is peopled.
Schaff, Philip. NPNF1-02. St. Augustine's City of God and Christian Doctrine. CCEL, 1890.
Notice how St Augustine has no qualms with the Earth being "scientifically demonstrated" to be spherical. All of his arguments in this chapter were merely that the other side of the sphere was not populated.
In any case, St Augustine was more explicit in the lesser known The Literal Meaning of Genesis:
Although water still covered all the earth, there was nothing to prevent the massive watery sphere from having day on one side by the presence of light, and on the other side, night by the absence of light. Thus, in the evening, darkness would pass to that side from which light would be turning to the other.
Genesi Ad Litteram. Paulist Press, 1982.