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Hopefully you insured it for the value of the amount you returned and they will look at that! Did you make a copy of the receipt?
Wow... this is a lesson to all of us who return things! I know you are sick until it gets resolved! I have some returns in transit now, so it could happen to any of us, i guess.
Please, let us know what happens.
 
I would call the store manager right away and explain the situation. Also, file a claim with Fedex. Tell the manager that you have all the shipping info and proof that is required and that it is going to be investigated and although you'd hate to think of employee pilferage, but if that is the case then you will want to prosecute to the full extent. That way the manager thinks you know what your talking about and will get nervous and hopefully do something about it. Good luck!!
 
Poor you, now you get to worry about it until it's resolved. I hope it works out okay for you, it sounds like it should do if you shipped with Fedex, but you're going to just have to take a deep breath and jump through all the necessary hoops to pursue it until you get satisfaction. Good luck.