I asked a question on StackOverflow, and later discovered that what I thought was happening wasn't; because of this, my question was inaccurate and irrelevant to the issue. What should I do to the question? Should I delete it?
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You should write an answer to the question describing what the resolution was. Either explain what the false assumptions were, what information was missing from the question, what error you made in diagnosing/replicating the problem, what seemingly unrelated event changed to fix the problem, etc.
You should mark the answer that you've written as the accepted answer because it is the solution that you're actually using, and it will help emphasize to future viewers what actually happened.
Given that, by definition, the question clearly wasn't answerable, it should also probably be closed as "not a real question" or "too localized". You could, if you wanted, flag the question for moderator attention, use the "other" reason, and ask that the question be closed on that basis.
Delete it is the way to go. There is no need to keep invalid questions on the site.