have discarded of the box in which it came
Doesn't say how much the fee is but:
"Missing Item or Damaged Product Fee
A missing item or damaged product fee may be charged for any product missing the original box, packaging material, contents, accessories and/or manuals; any product not in "like new" condition."
i have already filed the rebate with MS! does this matter?
"Any product that was purchased when a mail-in rebate was available on the purchase is subject to having the amount of the rebate deducted from the refund amount."