I also just experienced this same problem, but hadn't changed my URL or anything. I just had deactivated Jetpack and reactivated it from the plugin manager. After finding this post, I looked at the database and found that Jetpack had given itself an new blog ID, which is why I didn't have any of my previous stats. I had the old blog ID saved, so I just edited Jetpack's options and gave it my old ID, and now all my stats are back. Thanks for the information so that I could fix this.
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