Can't I just define say a start handler with XML::Parser that adds non self ending tags to an array and then define an end handler that removes tags from the same array. Then maybe at the end of parsing all that would be left in the array would be those tags not found by the end handler and these tags could be added to the end of the xml file in reverse order with last in first out?
That's basically what I was trying to suggest. SAX is one common stream-based parser that people coming from a non-Perl backgrounds might know. XML::Parser is another stream-based parser which is, IMHO, easier to use.