Well, I'm still not sure that I really grasp what it is you're trying to do, but maybe this will be of some help. Changes the lines in the second file if the first field in the line is contained as the first field in a line in the first file (combining data from the two files), or does nothing if not:

#!/usr/bin/perl
use strict; use warnings; use feature 'say';
use Data::Dumper;

my @data1 = (
    ['Aspergillus_clavatus_1',  'XP_001276684.1', 'pectate lyase, puta
+tive [Aspergillus clavatus NRRL 1]'],
    ['Aspergillus_fumigatus_2', 'XP_001276694.1', 'conserved hypotheti
+cal protein [Aspergillus fumigatus NRRL 1]'],
    ['Aspergillus_flavus_3',    'XP_001276726.1', 'tyrosinase central 
+domain protein [Aspergillus flavus NRRL 1]'],
    ['Aspergillus_terreus_4',   'XP_001276738.1', 'endoglucanase, puta
+tive [Aspergillus terreus NRRL 1]']
);

my %data1;

for my $record ( @data1 ) {
    my ( $old, $new, $text ) = @{ $record };
    $data1{ $old } = { new => $new, text => $text };
}

my @data2 = (
    ['Aspergillus_clavatus_1', 'Aspergillus_flavus_198', 'Aspergillus_
+terreus_166', 'Aspergillus_fumigatus_2'],
    ['Aspergillus_clavatus_1', 'Aspergillus_flavus_3',   'Aspergillus_
+terreus_4',   'Aspergillus_fumigatus_2'],
    ['Aspergillus_clavatus_3', 'Aspergillus_flavus_198', 'Aspergillus_
+terreu_166',  'Aspergillus_fumigatus_16']
);

my @results;

for my $row ( @data2 ) {
    my $lookup = shift @{ $row };
    push @results, exists $data1{ $lookup } ?
        join "\t", $data1{ $lookup }->{'new'}, $data1{ $lookup }->{'te
+xt'}, join "\t", @{ $row } :
        join "\t", $lookup, join "\t", @{ $row };
}

say Dumper \@results;

__END__
[download]

$VAR1 = [
          'XP_001276684.1    pectate lyase, putative [Aspergillus clav
+atus NRRL 1]    Aspergillus_flavus_198    Aspergillus_terreus_166    
+Aspergillus_fumigatus_2',
          'XP_001276684.1    pectate lyase, putative [Aspergillus clav
+atus NRRL 1]    Aspergillus_flavus_3    Aspergillus_terreus_4    Aspe
+rgillus_fumigatus_2',
          'Aspergillus_clavatus_3    Aspergillus_flavus_198    Aspergi
+llus_terreu_166    Aspergillus_fumigatus_16'
        ];
[download]

Hope this helps!