You need to create a new PPI::Document object for each here-doc. I say that because I tried calling two here-docs, but PPI would only give me one. Also, I couldn't replicate your output. How did you replace 'Something' with 'else'? I would modify the docs like this: 
#!/usr/bin/perl 

use strict;
use warnings;
use PPI;
use PPI::Dumper;

my $data;
($data = <<'ENDOFSQL') =~ s/Something/else/;
Something
ENDOFSQL

my($Document) = PPI::Document->new(\$data);
my $Dumper = PPI::Dumper->new($Document);
$Dumper->print;

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In reply to Re: Problem with PPI HereDoc's by Khen1950fx
in thread Problem with PPI HereDoc's by clueless newbie

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