Here is the saga of the lost files.
I have been in the habit of using the Safari feature on my iPad to "Save PDF to iBooks" for articles that I want to preserve.
They are the only files stored in iBooks.
When I did my backup and restore to my new iPad, all those files did not get backed up and restored.
I had in the past used iExplorer to extract the PDFs from iBooks. They ended up stored in the system /Applications directory on my MacBook Air. I don't know why they ended up there. I found the user interface of iExplorer to be really unhelpful. So I ended up doing the wrong thing. My mental model of things is based on the Unix way, not the Macintosh way, and this got me into trouble twice in this saga.
Yesterday, while trying to get the files out, I moved them from the /Applications directory to a temp directory. Well, I wanted to do a Move, but Finder wouldn't do a Move, probably because it was from a system directory, so I copied the files to the temp directory. I checked them, viewed them, great. I transferred them to a USB stick. Then I deleted them from the /Applications directory. And then, stupidly, assuming that they were safe on the USB stick, I emptied Trash.
When I copied them from the USB stick to my Linux desktop, I checked them once more and found that I had a whole bunch of small files that were aliases. They were aliases to the original PDF files that had been on my MacBook Air, in /Applications, which I had just now deleted and then erased from Trash. Gone, gone, gone.
Today, I took my MacBook Air to work and plugged in my Time Machine drive, and checked to see if I had done a backup after using iExplorer. Amazingly, I had. I restored all the PDFs to a temporary directory, then copied them to a USB stick, and moved them to my Linux desktop. And yes, I had the real files, the PDFs, not aliases.
So now I have got back 400+ of my PDFs. I am probably missing about 10 files that I saved since that backup. I have the links to them, so I can recreate them. I won't delete the files from my MacBook Air just yet. I'll leave them there for a while, and let Time Machine back them up again. Just in case. I can clean things up next week when I am well settled in with the new iPad.
I am much happier today. Going forward, I will not use iBooks any more for this. I will use Readdle PDF Converter which will save to DropBox.