Here is an XML::Twig that will be easy on your RAM (only one journal is in mem at any given time).

 #!/usr/bin/perl -w
use strict;

use XML::Twig;

# you will actually get the list from a file
my %to_remove= map { $_ => 1 } ( "1742-7061");

XML::Twig->new( twig_roots => { journal => \&journal },
                pretty_print => 'indented',
              )
         ->parse( \*DATA)  # replace by parsefile( "file.xml")
         ->flush;

sub journal 
  { my( $t, $journal)= @_;
    # this works if the ISSN is a child of journal,
    # otherwise it might be a little more tricky.
    if( $to_remove{$journal->field( 'ISSN')})
      { $journal->delete }
    else
      { $t->flush; } # ouput and cleanup memory
  }

__DATA__
<bulk>
  <journal>
    <full-title>Acta Biomaterialia</full-title>
    <alternate-title></alternate-title>
    <ISSN>1742-7061</ISSN>
    <E-ISSN></E-ISSN>
    <vol-year></vol-year>
    <iss-vol>1</iss-vol>
    <start-date>01-01-1974</start-date>
    <target>
      <siteID>1</siteID>
      <rank>200</rank>
      <activate></activate>
    </target>
  </journal>
  <journal>
    <full-title>Acta Biomaterialia</full-title>
    <alternate-title></alternate-title>
    <ISSN>1743-7061</ISSN>
    <E-ISSN></E-ISSN>
    <vol-year></vol-year>
    <iss-vol>1</iss-vol>
    <start-date>01-01-1974</start-date>
    <target>
      <siteID>1</siteID>
      <rank>200</rank>
      <activate></activate>
   </target>
  </journal>
</bulk>
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