We move the .FAILED files to another folder, then rename to .PDF again.
The Syslog error 88 message will give you the page of the PDF that the indexing failed on.
Our PDFs are container files with multiple bills or letters. We use the full Adobe tool to extract the bad pdf from within the container, and then re place the new PDF for loading. If the file is good, except for the extracted pages, it loads. We forward the bad bill or letter file to the developers for resolution.