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."