Unfortunately some problems have slipped through because your code doesn't use strict; If you did that you'd see that the $line3 variable is undefined, and others lack lexical scoping.

Update:

Felt a bit guilty for the brevity of my original answer, so here is a quick example of code that works to produce the output you were expecting. It may need some tweaking as you see fit

use strict;
use warnings;

# Load the acceptable ids from file2 into a hash
my %ids;
open my $idfile, '<', 'file2' or die $!;
for (<$idfile>) {
        $ids{$1} = 1 if m/Accept\s+=>\s+(\S+)/;
}
close $idfile;

# Scan file1 printing each line where the ID matches one found in our 
+hash
open my $datafile, '<', 'file1' or die $!;
for (<$datafile>) {
        chomp;
        my ($id) = m/ID\s+(\S+)/;
        print "$_\n" if exists $ids{$id};
}
close $datafile;
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Output:

ID John06/ext $work(b05bfn00ld0p7)/b05bfn00ld0p7 ; #<= b05bfn00ld0s0 S
+ize:INFINITY
ID lily099/poli $work(b05bfn00ld0p7)/b05bfn00ld0p7 ; #<= b05bfn00ld0s0
+ Size:INFINITY
ID lily099/poli $wwrk(b05bfn00ld0p8)/b05bfn00ld0p8 ; #<= b05bfn00ld0s0
+ Size:INFINITY
[download]