This happened recently: a user removed his account and some users (including me) lost some rep points from votes coming from that (ex-)user. Is this 'standard procedure'? Do the reps associated to the votes all go
(source for poof: here)
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As the others said, all the votes ( upvote or downvote ) get reversed. You can see the proof in your reputation history. Just go to reputation tab and there will a option to select at the last just like below, just tick that mark,
when you will tick it, you can see the removed votes from your reputation ( in case the use who vote up/down your question/answer is get deleted ) just like below image.
Yes, any rep you earned by votes from a user that later deletes their account all goes poof.
Don't sweat it. It happens to the best of us. In the grand scheme of things, this happens very rarely and will be a very small percentage of your reputation (unless the only thing you ever did is get rep from that user!).
This is actually by design and for the best. The most frequent reason a user gets deleted is not because they decided to leave the system but because their account got identified as a duplicate or sock puppet created specifically to create forged votes. The fact that these votes are removed from the system is a GoodThing(tm).
All votes are currently deleted when a user is deleted, both upvotes and downvotes.
I don't think this is the right behaviour for users that request self-deletion and I posted a feature request to change this a while ago: Don't throw away all votes when a user is deleted.