Is it the name that doesn't exist or a specific document? Is it possible the document was never filed by the bank or filed but never recorded by the county? I know of one incident where a deputy clerk in one of the counties I work was fired for not doing her work. When they emptied her desk they found many documents she had never recorded. It seems when her workday would end, she would just stuff any documents that she had not had time to record into a drawer and forget about it.

 I certainly wouldn't agree to remove your notation from your report. You were right to note this and it may be your best protection. You might even consider getting a printout of the computer index and a copy of the relevant pages of the book index so you have proof the name doesn't appear.  It is hard to alter the books without leaving some sign but in the case of computer a corrected error would leave no trace and you could be blamed.