I was a little surprised to have found that I lost 132 rep due to some user that was deleted (!). What I do not understand, however, is that this has happened on a day that I am (so far) 17 votes beyond the 20 of the daily limit, and yet I still lost the rep. How does this work?
When a user is deleted, his up/down votes are undone.
This happens as often as users request to be deleted.
That's by design. You can only recover these points by accepted answers, bounties, etc.
Anything which isn't limited by the cap itself.