reference of "that"
"Followers of Pythagoras acknowledged that nature was in a perpetual state of flux, change or metamorphosis, but this in itself was manifest of a kind of eternal constancy."

Does "this in itself" refer to "the state of nature (being in a perpetual state of flux, change or metamorphosis) or "nature" itself?

Question

reference of "that"
"Followers of Pythagoras acknowledged that nature was in a perpetual state of flux, change or metamorphosis, but this in itself was manifest of a kind of eternal constancy."

Does "this in itself" refer to "the state of nature (being in a perpetual state of flux, change or metamorphosis) or "nature" itself?

Answer

It refers to the "state of flux."

"In itself" is used for emphasis. It conveys the idea "This sounds like a contradiction. It is subtle and paradoxical truth, not a mistake in wording."

The debate is whether nature is in flux or constancy. Someone says "You are wrong, nature is not in a state of eternal constancy, it is always in perpetual flux." The Pythagoreans retort "That's true. But it does not refute us, it actually proves our point. 'Perpetual flux' is a kind of constancy."