Here's a perl script that you could run with one or more file names as command line args, and each file would be edited:

#!/usr/bin/perl

use strict;

for my $file ( @ARGV )
{
    {
        local $/;
        open( my $fh, "<", $file ) or do { warn "unable to read $file\
+n"; next };
        $_ = <$fh>;
    }
    s/( \{ \s*
          header\("Window-Target:\s*_top"\); \s*
          header\("Location:\s*index\.php"\); ) \s*
        \}
     /$1\n exit;\n}/gx;
    {
        open( my $fh, ">", $file ) or do { warn "unable to edit $file\
+n"; next };
        print $fh $_;
    }
}
[download]

Note the following:

• using the "x" modifier (so the regex can be arranged more legibly)
• using capturing parens in regex to simplify replacement
• using "\s*" to match all the (potentially variable) white space (this is the only way you must use something like this to match white space when using the "x" modifier, but you should be handling white space this way in any case)
• using lexically-scoped file handles in minimal blocks
• using local $/ for slurp mode (in same scope as file handle)
• skipping files that can't be read or written (and showing a warning each time)
• if the script is run a second time on the same file, it'll just rewrite the file without changing it (because the regex won't match)

And if I'm taking the trouble to store this edit operation as a little perl script all by itself (which I think is a Good Idea), I would also take the time to add some POD commentary to say why I wrote this script in the first place.