I think you're wanting to do too much in one step. I'd do it the following way :

sub unlink_exists {
  my ($filename) = @_;
  if (-e $filename) {
    unlink $filename or die "Couldn't remove '$filename' : $!\n";
    print "Removed $filename\n";
  };
  return 1;
};

unlink_exists($_) for ($f,$a,$scratchfile,$fasta_output);
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This will, of course print up to 4 lines instead of one line, but it's much more readable in my opinion, and also provides you with much better diagnostics.

It's not possible to write unlink_exists as a function that returns true if the file was detected and successfully removed like the following :

sub unlink_exists {
  my ($filename) = @_;
  my $result = -e $filename;
  if ($result) {
    unlink $filename or die "Couldn't remove '$filename' : $!\n";
  };
  return $result;
};

if ( unlink_exists($a) || unlink_exists($f) ... );
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because Perl does not fully evaluate expressions - it stops as soon as the expressions value is determined.

perl -MHTTP::Daemon -MHTTP::Response -MLWP::Simple -e ' ;    # The  
$d = new HTTP::Daemon and fork and getprint $d->url and exit;#spider
($c = $d->accept())->get_request(); $c->send_response( new   #in the
HTTP::Response(200,$_,$_,qq(Just another Perl hacker\n))); ' #  web
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