Due to a problem in the Quartus® II software version 13.0 SP1 and earlier, in the Convert Programming File utility, the Enable decompression during Partial Reconfiguration option is not restored when you open the Conversion Setup File (.cof).
To work around the problem, turn on the Enable decompression during Partial Reconfiguration under the SOF File Properties window after you restore settings from the .cof.
This problem is fixed starting with the Intel® Quartus® Prime Standard Edition Software version 17.0.