>I've noticed that the redirect doesn't want to over-write files which have
>been hidden,

That's an operating-system behavior, not anything Xalan is doing:
     D:\>echo test1>foo

     D:\>attrib +h foo

     D:\>echo test1>foo
     Access is denied.

Write an extension that let you manipulate the filesystem, or set up a
wrapper around Xalan that un-hides and re-hides the files, or ask yourself
whether the file should really be hidden in the first place.

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