Your post would seem to indicate you have managed to pull generated output files into your source and replace the source files with them. Ouch!
If you have a backup, definitely time to restore.
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Thanks, Captiv8tor. You've confirmed my worst fears about "contaminating" our version control files. I am up against a release deadline and I don't feel I have time to pull 300 topic files out of subversion and do a new build of Help. Do you have any other advice? Can I delete the whnjs and whskin_blank files from the lists in RH? Thanks.