I'm almost certain the refund was in fiat since the prices on cointerra's site are all in USD and because they use bitpay to process payments and automatically adjust the BTC price based on the current exchange rate.

I wouldn't complain if I'm wrong though.

Update 2013-11-11: Peter from Cointerra finally got back to me and said they will send me a refund in the form of a check for USD.