The XML::XPath::XMLParser::as_string treats all nodes the same, even if you're working with the root node. Therefore it does not contain the header information of a full xml document.

If you want the header, just capture it independently and print it out.

use XML::XPath;

use strict;

my $filename = 'test.xml';

my $header = do {
    open my $fh, $filename or die "$filename: $!";
    <$fh>;
};

my $xp = XML::XPath->new(filename => $filename);
$xp->setNodeText("/project/dependencies/dependency[version='1.0']/vers
+ion", 2.0);

open my $fh, '>', $filename or die "$filename: $!";
print $fh $header;
print $fh XML::XPath::XMLParser::as_string($xp->findnodes('/'));
close $fh;
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Also, use <code> instead of <pre> tags per How do I post a question effectively?.