Sure mate. But this time you gotta promise you will read open's docs :).

First point: when you read the file, and since you are adding more lines, you have to get all those lines. Also, you are appending a new line to the end of each conf variable, so there is the need to chomp that new line.

if (-f $file) {
    open CONF, "<$file";
    my @contents = <CONF>;
    close CONF;

    foreach $content (@contents) {
        my @config = split /-/,$content;
        if ($content =~ /DEFAULT_IN/) {
            $default_in = $config[1];
            chomp($default_in);
        } elsif ($content =~ /DEFAULT_OUT/) {
            $default_out = $config[1];
            chomp($default_out);
        }
    }
}
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Second point: Writing the info back to the file. I don't know what those browse methods are, but if you need to write in two separate steps, then you'll have to write all the info both times.

print CONF "DEFAULT_IN-$def_path\nDEFAULT_OUT-$def_path_out\n";
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As a side note, you should look for a way of being able to write only if any of the paths actually changed.

if( ($def_path ne $default_in) || ($def_path_out ne $default_out) ) {
    # at least one of the values changed, write both
}
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update lil_v updated his node, so now this doesn't make much sense.