I'm confused why people are finding this difficult. It's obvious from the forum posts here that there have been some of these sent out in error. If you've already paid the fee, but received this email, just call CIC and get them to check that your payment is on file. If they say it isn't, tell them you'll send the receipt from the first time you paid it (quote them the payment number on the phone).
Paying this twice just because they sent you an email is crazy. Call them and sort it out. You don't have to throw $490 away because of a computer glitch.
Oh, and if you haven't paid it yet, then just go ahead and pay it whenever. I didn't wait for the email during my process, I just paid it and emailed the receipt. All went totally fine. Might have even potentially made things speed up.