If it were me, I would dispute the credit card charge as no services were provided. Czech Air is responsible for restoring you to the same position you would have been otherwise, by paying you cash for your economy flight minus the cost of the ticket you originally bought (assuming you successfully dispute it). If Expedia screwed something up, then Czech Air should get it from them.

Did you buy this from the U.S. Expedia.com with a U.S. credit card in the U.S.? Change as appropriate; it might be important information.