The $FWDIR/conf/IPtoCountry.csv file comes with the installation, and will not ever be changed.
The file is downloaded from the Download Center every 24 hours to $FWDIR/tmp/geo_location_tmp/updates, and loaded onto the kernel. The file in $FWDIR/conf is used only if there is no file in $FWDIR/tmp/geo_location_tmp/updates.
If the file cannot be downloaded, the existing file (in $FWDIR/tmp/geo_location_tmp/updates) is used.
The file in $FWDIR/tmp/geo_location_tmp/updates will always be newer than the one in in $FWDIR/conf (unless no file was downloaded).