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if (-f $file) {
    open CONF, "<$file";
...
        }
    }
}

print CONF "DEFAULT_IN-$def_path\nDEFAULT_OUT-$def_path_out\n";

if( ($def_path ne $default_in) || ($def_path_out ne $default_out) ) {
    # at least one of the values changed, write both
}