Okay so Apple doesn't let you easily move files from the iBooks app on iPad even though it seems like it should be no problem to do. It is possible however with a little trick. First, I'd having dropbox or google drive loaded and logged in on your iPad. Once those apps are set up, if you go into the Files app and tap on the three dot circle button (next to the word "browse" in the column that says "locations" and "tags" on the left side of your screen). Then tap edit. you will see dropbox or google display (make sure the slider for whichever you chose to use is green for on). Then go back into iBooks and go into your library. Tap on "collections" and select "PDFs" (this will cause only your PDF files to be displayed). Then tap "edit" at the top right of your screen, then "Select All" at the top left. tap and hold on a PDF until it gets slightly bigger, then drag your finger slightly in any direction. You will see your PDFs bunch up and a little blue number in the corner of them (which displays the number of PDFs you have, I guess around 700). Keep holding those documents. Then with your other hand, navigate back to the Files app once again. You should still be holding the PDFs as you get there. Once in the files app, select either dropbox or google drive (whichever one you picked earlier) and drop the PDFs on the right side of your screen. You should then see them start to copy themselves. After that's done, you can now put them wherever you'd like from any device.
It really shouldn't have to be this complicated, but this is the only way I can seem to do it. Let me know if you need clarification with anything :)