After updating Xcode via App Store, I now have 2 Xcode apps in my launchpad. I can delete the new one by holding my mouse button down and clicking the x that appears, but only for the new one.
The easiest way to fix this is to head to your applications folder, (Using the menu bar, not a dock folder) and manually moving Xcode to your trash. After that, open launchpad and let it update. Both Xcodes will be gone. Then open your trash and right click Xcode, select Put Back. Voila, you fixed your problem and didn't even have to re-download!
If moving the app to trash and back does not solve the problem, try this command in the Terminal before you move the app back from the trash:
killall Dock
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