The same thing happened to me earlier this year. I got Dish to agree to replace a defective purchased ViP612 with a purchased ViP722k, and I had activated another purchased ViP612 while I was waiting for the installation of the ViP722k. The installer checked and told me that there was no need to return either ViP612 (I deactivated both of them when the ViP722k was installed.) so he did not take either one with him. Then, months later, Dish sent me an email just like the one they sent you.
After getting that straightened out, and getting Dish to send me a shipping label so I could return the defective ViP612 and get the $199 charge credited back to my account, I later purchased a Wally from Dish as an additional receiver. They set up the order as a replacement receiver for my existing purchased ViP211k, and the Wally came with a shipping label and instructions telling me to return the ViP211k or I would be charged a non-return equipment fee. This ticked me off, and DIRT could not help with this issue, so the DIRT member gave me the phone number for the Office of the President department. When I called that number, the representative told me that he would monitor my account to make sure that I would not be charged that fee. I have not been charged a fee in this case. However, it still sucks that Dish threatened to charge the fee, that I have to watch my account like a hawk to make sure that Dish does not screw anything up, and that I had to go through so much hassle because of Dish's mistakes.