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We (Rob, Colen and I) tend to edit most of our data files in an XML editor. When we do so, we use the XML comments mechanism rather than the comments mechanism that you can access from within the editor, and like to create a pattern of indentation that makes the data easier to read within an XML editor.
When you save a file in the HL editor, all that information and organization is stripped away. So, distinguishing the files meant to be edited in an XML editor (.dat) and the files intended to be edited in the HL editor (.user) means that the editor can be set up to only open .dat files in read-only mode (which means that if I change something on the Class tab, I can test it without using the new class wizard to create a class to test with, by opening one of the existing classes as read-only file).
Also, as I understand the mechanism, if HL detects some problem in a .user file while compiling its files that it can't resolve, it can shut out all the .user files and load HL in safe mode. That way, a user who isn't familiar with XML editing can fix the errors, and get their files back in working order.
So, there is actually no difference between the contents of a .dat file and a .user file, but in general, the users should only be working with .user files. Just change the file extension if you still have any .dat files in your system.
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