I accidentally duplicated app file? and can't get rid of the duplicate

I think I've done something silly, but I don't know how to fix it.
I suddenly wondered if I could organize FaceTime and Skype into a folder on my dock so that they wouldn't be taking up two slots for essentially the same function. In applications, I made a folder and dragged each of them in, but FaceTime seemed to copy/duplicate itself rather than moving (I guess because it's hardwired into Lion). I realized I couldn't put the folder in with the rest of my apps on the dock, only to the side with my downloads folder, so I wanted to put the apps back onto the dock individually and delete the folder. I dragged FaceTime from applications back onto the dock, worked fine, and I put the folder in the trash. When I went to empty the trash, it said the item FaceTime was in use, and when I opened up the trash, the icon for FaceTime was the little missing-application-image icon.
I dragged it from the trash to my desktop, then tried to put it into my applications folder to see if it could be deleted by putting it near the "real" application, to which the system responded, "FaceTime can't be modified or deleted because it's required by Mac OS X." So I can move it between the trash and the desktop, but I can't put it anywhere else or delete it. Get info says its file kind is an application, name being FaceTime.app, but its file size is only 78 KB, compared to the 15.6 MB identically named file in my applications folder.
What on earth did I do, and how do I get rid of this ghost that thinks its an app? If anyone can help, thanks.

Why don't you proceed with update and see what happen.

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