Why did my rep go down? Is it because I recieved upvotes for answers that were later deleted (say, because the question I answered was deleted)? Is this the same thing that would happen during a site-wide rep recalc? I'm just curious (and tired, so I probably missed the entry in the manual about this feature).
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Yes, it is the same as what would happen during a site-wide rep recalculation.
Your reputation would go down for the reasons detailed in the blog