my @dat_files = <$board_dir/*.dat>;
$q = 0;
foreach (@dat_files) {
    $number;
    $number = $_;
    $number =~ s/\/var\/www\/cgi-bin\/2930forum\/data\///g;
    $number =~ s/\.dat//g;
    open THREAD, "$_" or die "Can't open .dat file: $!";
    $x = 0;
    while (<THREAD>) {
        $thread_data[$x] = $_;
         $x++;
     }
     close THREAD;
     foreach (@thread_data) {
         @details = split /\|/, $_;
         if ($details[4] =~ m/\Q$in{for}\E/i) {
             $found[$q] = $number;
              $q++;
         }
    }
}
[download]

This code has a couple of problems. One is that the handling of filenames, particularly the method of extracting a number from them, is highly suspect. Once you think you've extracted $number, try printing both the full filename and $number.

It looks like you're trying to accumulate a list of thread nubmers that contain matches. Since you say that $thread_data[0] is the same as $number, this might be easier like so:

my @dat_files = <$bboard/*.dat>;
my %found = ();
foreach my $file ( @dat_files ) {
    open(DAT, $file) or die "$file: $!";
    while ( <DAT> ) {
        my @thread_data = split "|";
        if ( $thread_data[4] =~ m/\Q$in{$for}\E/i ) {
            $found{$thread_data[0]}++;
        }
    }
    close(DAT);
}
[download]

The keys of %found are now the thread numbers taht contain a match, and the corresponding values are the number of matches.