Repair Returned Without Accessories

You would have to try contacting support to see if there is anything they can do. http://support.xbox.com/contact-us The instructions for sending in consoles and controllers
do state to only send in the controller/console and nothing else as anything else that is sent in is not guaranteed to be returned.

you are not guaranteed to be returned any kind of special edition controller system you sent in for repair. They just sent you a refurbished one

You were told to remove all of the accessories before you sent it in which is why you got back or controller without joystick. they only return the base device

Thank you for your response. I have never opened my console. I have spent too much money on it to be doing something that I have no knowledge of on my console. If I had spent the 115$ it costs to repair or refurb then my seal and or serial number would be
in order. The seal on the back is still on the console and it's bent down so they have handled it. Why not just remove the entire seal if they want to make it appear as if I did something nefarious?

If the warranty seal within the console is found broken your warranty is void and MS will not accept your console for repairs for:

"Attempt to disassemble, decompile, create derivative works of, reverse engineer, modify, further sublicense, distribute, or use for other purposes the Services, any game, application, or other content available or accessible through the Services, or any
hardware associated with the Services or with an Authorized Device"

www.xbox.com/.../LiveTOU

The break of the warranty seal is a physical action, of tampering or opening the console, that voids any other service that might be provided to your console. At this point your only possibility is to seek help through a local repair service.

If you can't remove anything then it's still okay. They're going to wipe it when they get it either way.