Clicks should refer to the percentage to date in which case I would say that email A is doing much better than B (unless there are mitigating circumstances, like B doesn't have links or the links are incorrectly formed). You can confirm the numbers by creating an email link performance report in analytics, if you see different numbers then your email asking you to declare a winner might be wrong.
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Hey Mariel, with such disparate numbers I'd probably check the setup of the Champion/Challenger test. The first thing that comes to mind is that the challenger might not be sending -- which is what will happen if you have the test on a batch email. C/C will only work on triggered emails. You can confirm whether the email has sent at all via an email performance report.
You should keep a log in excel with the data from each week, which should help you understand this.