The 90 days is fishy, but a cheque, in itself, should be fine. For large amounts, it makes more economic sense for a merchant to issue a cheque for a refund (e.g., $0.75 bank fee for processing a cheque) vs a refund through VISA/MC (i.e., merchant fee applies). For example, if I were to issue a refund to a customer for $1000 on his/her VISA, I would also have to pay VISA a merchant fee (e.g., 2.5%) of $25. (That's on top of the merchant fees already paid on the customer's original purchase. Disgusting double-dipping...)