I'm pretty sure the change was neither arbitrary nor an attempt at modernisation. I don't have the books at hand at the moment, but I'm almost certain that JRRT himself changed his mind once or twice about "thou" vs. "you" in various places in the Narn.
(I believe (though I could be mis-remembering) that he originally wrote "thou" in some places but later began, but didn't finish, systematically changing every "thou" to "you". Presumably, in UT Christopher Tolkien left this as it was whereas in CoH he completed the systematic revision. I could be wrong about the details, though; I'll try to find the source when I get home.)
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