This has been greatly discussed on here in the past and below is a drawing I did some time ago.
The original Yamaha inspection notice said if the outside diameter of the shaft thread was more than 17.5mm, replace the 9mm nut with the new 12mm nut. If thread less than 17.5mm shaft to be replaced. The ones I have measured have always been round the 17.85 mark, so classed as O.K.
Under sized shaft threads was given as the reason for the nuts coming loose. I suspect in "some" cases it could have been incorrect assembly after fitting a new sprocket.
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When I spoke to Yamaha back then they said to torque the new nut to 90Nm. I believe there was a service note 2005-12A stating this but I have never seen it myself.
Final point don't forget to use loctite on the thread. That is part of the reason why a nut can be very tight to undo and not because it was done up that tight on assembly. (Unless it has already come loose of course!)