Have heard of this problem before, although I haven't had it happen to me!
The answer as I remember, was to delete the file the patch doesn't recognise i.e.
eng_help.txt from your base installation.
Then when you reapply the patch, it won't find anything to complain about. and will simply write in its own version of the file.
If that doesn't work, then maybe you have the wrong patch or something more radical ( along the lines Steve suggests ) will be needed.
Edit: Found original post!
http://www.subsim.com/radioroom/show...9&postcount=12
Hope this helps!!