I've gone back to select the correct PDF file but it doesn't seem to be re-setting

The second pass should overwrite pages already processed, but don't erase all previous data. To delete data capture, select all pages in the diagnosis frame (Data capture tab), and click Remove.

Is there any way for me to recover form this error?

If you kept the source file free from any changes, you can create a new project with the same source file: the subject should be exactly the same and your scans should be correctly processed.

Thank you for your help.

I tried the second option you described. I creased a new project from the original tex file. That seemed to go OK. I checked that the box code at the top was identical to the papers created in my original project. However, when I did the automatic data capture, I still received an error. The system says "1 scans were not recognized." When I select the show more (magnifying glass) button, a window with the title "Unrecognized scans" appreas with the message "Error loading scan/....path to pdf file...." And nothing more.

As far as I can tell the PDF file looks fine and just like any other file I've processed in the pass.

Any other suggestions?

I'll also mention that in the Command output details from processing the data file, that I get the following message:

Page : 0/0/0
Page : 0/0/0
Page : 0/0/0
Page : 0/0/0
ERROR: No layout for ID 0/0/0
===<analyse>=+1

Can you try again in debugging mode (from the Help menu) and post the resulting log file ?

I got it to work. I think that I was having disk space issues. Even though it worked, the system did a poor job this time (usually works very well) aligning the tick boxes. I needed to use the manual grading feature to go in a correct most of the tests. Perhaps there was an issue with the scan to the PDF file or maybe it was when I recreated to project.

Thanks for your help.