Try

#!perl 
use strict;

my $file2 = 'xname2.txt';
open IN,'<',$file2 or die "Could not open $file2 : $!";
my %file2 = (); 
while (<IN>){
  next unless /\S/;
  my ($FBgn) = split '\|';
  push @{$file2{$FBgn}},$_;
}

my $file1 = 'xname1.txt';
open IN,'<',$file1 or die "Could not open $file1 : $!";
while (my $line = <IN>){
  next unless $line =~ /\S/;
  for (split /\s+/,$line){
    next unless /^FBgn/;
    if (exists $file2{$_}){
      print join '',$line,@{$file2{$_}};
      delete $file2{$_};
    }
  }
}
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