Consider:

use strict;
use warnings;

my $man1 = <<MAN;
EXECUTE 1302267  help.txt
RUN     387469   help.txt
PIPE    34010402 run.exe
MAN
my $man2 = <<MAN;
EXECUTE 1302267  help.txt
RUN     387469   run.exe
PIPE    34010202 run.exe
MAN

my %manLu1;

open my $inMan, '<', \$man1;
while (<$inMan>) {
    chomp;
    
    my ($program, $size, $file) = split ' ', $_, 3;
    
    $manLu1{$program}{$file} = $size if defined $file;
}
close $inMan;

open $inMan, '<', \$man2;
while (<$inMan>) {
    chomp;
    
    my ($program, $size, $file) = split ' ', $_, 3;
    
    next if ! exists $manLu1{$program}{$file} || $manLu1{$program}{$fi
+le} == $size;

    print "1: $program\n";
    print "1: $file\n";
    print "1: $manLu1{$program}{$file}\n";
    print "2: $size\n";
}
close $inMan;
[download]

Prints:

1: PIPE
1: run.exe
1: 34010402
2: 34010202
[download]