Believe me I am very sorry about this happening to your company.  It has been a problem since computers were introduced to the Registry that misindexings get "fixed" without any notice to the public.  I actually take an exception for that issue on my report sheet.  Things were better when they were still printing out indices; then there was a paper trail- but who prints indices anymore.

At the moment Essex South does have a system where items that have been misindexed are fixed & then the information is entered into a log book.  The problem then is who gets stuck with the liability.  The Registry assumes no liability for errors even though I believe it should; so the examiner gets hammered instead. 

Hopefully this will all work out for you.