Originally Posted by ddjohn
Any ideas what might have gone wrong with the viewer and with the missing documents?
As already pointed out calibre's viewer tries to convert the file to html before viewing. This works better for some formats then others. Set calibre to not use the internal viewer for these pdfs.
There are only a couple of ways for documents to go missing and they all include the user deleting or moving them.
If you send them to your device via the dropdown arrow one of the choices is to send the book to the device and remove from calibre. Another possibility the user going behind the scenes and forgetting the file structure is actually calibre's library. If you physically moved, deleted or renamed the files then they would no longer be seen by calibre.
You can click the dropdown arrow next to the library icon go to Library maintenance and select check library. This will let you know if there are files in calibre's library directory that calibre's database is not aware of.