I don't think we can help much if you do not give us more details regarding the format of the XMLs, what kind of differences do you expect and how do you want to compare them.Maybe you could parse the file in chunks and compare the chunks, but if that's possible and how to do that ... that's a question.

You'd probably need to use a pull parser, XML::LibXML::Reader or XML::TokeParser, to be able to parse the two files at once and decide from which you want the next piece.