The DFU update you downloaded from the MiniDSO site is a complete ROM update, including the V1.64 Sys and the original FPGA and LOGO, along with their APP, that’s why the FPGA reverted to the original.
The DFU update you downloaded from the MiniDSO site is a complete ROM update, including the V1.64 Sys and the original FPGA and LOGO, along with their APP, that’s why the FPGA reverted to the original.