Hi Dr. Pearl,
Welcome to AC.
Well, not to sound like a broken record, but I agree with both Wendell and Indy. I am a bit at a disadvantage, because I don't import or scan to a chart. Are you using twain. I am probably showing my ignorance there as well.
I am not sure, but along the same lines as Wendell, I would be willing to bet that the problem is occurring at the very moment you finish scanning. In other words, I doubt you have scanned a document into patient 1003, and there is now a folder in the ImportItems folder with the name 1003 with a PDF in it. I just don't see how you could have that with a link to the Imported Items section in the chart and then lose the file or the link.
I would make a shortcut to the ImportItems folder on your desktop. Then after each scan check the folder immediately to see the subfolder with the patient's ID number and look in it for the PDF.
I am a little confused when you say the subtitle is there. Do you mean, when you look in the chart under Imported Items, you see a named folder or an icon for a PDF.
Make sure you check your permissions carefully to see that the scanner has full access to the folder.
You say that you can't do anymore scanning. I don't see why you can't. Simply scan to the desktop or wherever where AC is (doesn't have to be -- but it may be easier that way), and then manually import the file into the patient chart.
Which also brings up given that you are new to this, have you done a few manual imports? Clicked on import, browsed to a file, given it a subject and name, etc. Have you then seen the file there and been able to open it from there?
Finally, as Indy points out, any backups? Are you using AC's backup and including the imported items heaven forbid? And, in these troubleshooting situations, it helps to know more about the network, what clients, what is your server, P2P, etc.