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Sounds like you could use Readers for both files, reading them line by line, and writing out the result in whichever way you need to. Only thing to watch out for would be continuation lines, i.e. properties that span more than one line. Also, be careful to specify the proper file encoding.
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Adding to Ulf's post in a somewhat orthogonal but complementary way: consider using LinkedHashMap rather than Properties. This will allow you to maintain insertion order (of course you will need to decide which o the two properties fields comes first) while maintaining the basic contract of a Map (which Properties extends, and if you're using JDK 5.0 there's little reason to continue using Properties anyway). Ulf's post suggests how to read the file; this post suggests where to put the contents of the file after it's been read. Between the two, you may be able to achieve your goals.