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WAR is not "stored" for players, but is recalculated. Because of that, it can shift slightly for previous seasons as we do store data slightly differently (ie. we may use the MLB average values instead of AL-only average values).
But I would certainly expect that variation to be only fractions of a point. The only other thing I can think about is if you are not storing career fielding stats (Game Settings -> Players & Facegen), then obviously the defensive components for players would not be accurate.
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