How to recover PDF files from iPad

Just recently I had the unenviable problem of a hard disk failure on my Mac Book Pro
Now after a data recovery specialist did his work, I just may have most (all?) of my data back but what was lost was folder structure and in a lot of cases filenames as well (last backup was unfortunately a good 6 plus months ago)
So right now I'm going through the 2nd part of data recovery whereby I'm finding files of all extensions depending on whats important and what I'm doing right now (Mac Book also operates as a small business)
What would be good is to take some efficient shortcuts where it comes to what is on my other devices
In the case of my iPad I keep a lot educational PDF's within iBooks that were purchased outside of iBooks and it would be great to get these PDF's and put onto my mac book pro
A long winded version would be that I can email them back to me and then install on the hard drive but there are a couple hundred
Would you please have any suggestions as to how I can recover these files back to my empty laptop?
Gracias
M

Thanks - I've gone into settings on my iPad for both iCloud and iBooks and can't see any settings that say that these PDF documents are/can be backed up there?
If I go into iBooks on my mac book (yes-running Mavericks) then I can see all the collection titles I've created to file these PDF's but none of the files underneath them?
The purchased ones from the iBooks store naturally show up but my other PDF's don't

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