The best way to handle xml files is with a module. If you look on CPAN you find some like XML::Simple or XML::Twig

Also you should change your data type to store your keys. Use a hash instead of an array. Why? Because a hash already makes sure that there no key can be repeated. And searching for a key is a lot faster than with an array.

If you don't know how to use a hash, read the docs. It is nearly as simple as an array, but sooo much better for most problems

UPDATE: This is not a code writing service. The script you had was not bad as a first draft. Adapt it a bit, debug it and it should work. Here is a hint:

#Suppose you got a new XML key and value read from the file in $key an
+d $value

if (not exists $hash{$key}) {
     $hash{$key}= $value;
}
else {
    #drop key
}
[download]

This is already the meat of your hash handling.