According to Magnepan, the break in is a consequence of thermal cycling. I think you'll find that once they're broken in broken in, the effect will be long lasting. I don't know if it's permanent, though, I've seen varying opinions on whether they have to be broken in again when they've been unused for a while.
Break-in with electronics, where it does occur, should proceed very rapidly -- basically, it's a matter of electrolytic caps reforming after a period of disuse. (Though there are those who say otherwise.) I think it's possible to confuse break-in with the fact that the ear accommodates to new equipment or acoustics over a period of hours and days. The ear will "tune out" some forms of distortion and it's easy to mistake this for improvements in the equipment itself.
In the case of elastomeric mechanical devices like loudspeakers, though, break-in is a real and measurable phenomenon that takes a while to occur.
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