Solution:
To bring the LatticeECP3 IO Protocol evaluation board back to the original factory programming, go to this page on the Lattice site:
http://www.latticesemi.com/en/Products/DevelopmentBoardsAndKits/LatticeECP3IOProtocolEvaluationBoard.aspxThen click on the icon labeled "Default Programming Files" and save the ECP3_IOP_Rev_C_Default_1.2.ZIP file in a temporary directory. Now unzip the file and follow the instructions in the top directory to restore the programming of either or both the Lattice ispPAC (U17) or the Lattice MachXO (U5) devices. The LatticeECP3 (U7) default programming files are also included in that file set.