It looks like you are working with an XML file so you should probably be using something like XML::Twig or XML::TreeBuilder to manipulate the data.

Aside from that, the first thing to do is get your code passing strictures. As presented there is an unquoted " that generates an error. Using qq instead of a bare " quoted string would help a lot. eg:

print OUTFILE qq~<APPLICATION APP_FILE_PATH="xxxxxx" CONFIG_FILES="xxx
+x...~;
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