Magnets can be demagnetized if overheated to near their melting point (unlikely in an oil filled engine) or are subjected to lots of strong shocks repeatly. Either of these can allow the ions to realign causing the magnet to loose strength.
Still, considering that bikes have always used magnets in their alternators (I think) with long term good results. While possible I kinda doubt that's your problem.
Also, if you're having low output from the stator, you can check to see how "centered" the stator coils are inside the rotor. The stock mount does not center the coils... When I did the tuxedo mod, and made the mount for the stator, I set it up where the coils were deeper inside the rotor, thus centering the coils more.
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