If one has already joined several sites, and then achieves 200 reputation on a site, will this automatically +100 the other sites? Or is the +100 only for newly joined sites after having 200 reputation?
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You need to unassociate your account that recently hit 200, then re-add it, and you should get the 100-point association bonus.
EDIT: Note that you can only get the 100 bonus once on a given site, even if you associate it with multiple other sites that have over 200.