If I delete my question with some up-votes, what will be the effect of this on my reputation? Please don't answer with "Why should you delete a question with up-votes?". I just want to know the SO system.
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At the first reputation recalc that occurs you lose all rep from deleted posts with upvotes and you gain all points lost through downvotes on the deleted posts.
I've only had one rep recalc in about 6 months, so results may vary. You might not see a rep hit for quite some time. But take into account, you will lose all rep received from deleted upvotes eventually.