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And to confirm, it's not the freehub either, just removed that along with the cassette and the qr stuff, and spinning the flywheel by hand also makes the knocking happen, so it's deffo something internal.

After an hour on the turbo tonight, fairly steady state, a loud knocking started. It's not the cassette and appears to not even be in sync with the fly wheel. I can spin it up with it knocking, stop pedalling and as the flywheel spins down, the loud knocking still occurs, so it's something internal....