If I understand what you are trying to do, you probably need a single HoH (hash of hashes) structure rather than several different hashes. Something along the lines of

use strict;
use warnings;

my @filesThisRun = (qw{file1 file2 ... fileN);
my %fileInfo = ();

foreach my $file (@filesThisRun)
{
    open my $lookupFH, q{<}, $file
       or die qq{open: $file: $!\n};

    while (<$lookupFH>)
    {
        my ($refName, $refID) = (split m{\t})[3, 4];
        $fileInfo{$file} = {$refID => $refName};
    }

    close $lookupFH
       or die qq{close: $file: $!\n};
}
[download]

That gives you a hash keyed by file name with the value for each file being an anonymous hash of refID/refName pairs. If you need the count number rather than the file name as the key then increment a count each time through the foreach and use that as the key instead of the file name. To access the refName for file "file2", refID "XX" you would do

my $queryFile = q{file2};
my $queryRefID = q{XX};
my $resRefName = $fileInfo{$queryFile}->{$queryRefID};
[download]

I hope this is of use.

Cheers,

JohnGG