I’ve got it. I think. Took me a long time but I think I have worked out what’s happening. Hopefully this might be helpful to someone else.
First of all I noticed locking the file in the Finder seemed to stop Preview remembering a different page. So if I opened the PDF on page 1 and then scrolled to page 10 it wouldn’t remember the PDF was on page 10 anymore when the file was closed then reopened. That was the first clue.
I then used fseventer which monitors file changes in real time and I was surprised to see that opening a PDF in Preview, scrolling to a different page and then closing the PDF updated the file itself. It doesn’t literally register a time change in the Finder, the date stays the same, but fseventer threw up the clue ‘Modified xattr’.
Ok, I dimly remembered some mention of this feature called extended attributes from years back, it seems to function like yet another kind of metadata but that’s quite separate from ‘normal metadata’, and now I'm reading was a replacement for the old resource forks in OS 9. Running $mdls (used for normal 'metadata') in Terminal won’t show extended attributes.
You have to use the command $xattr to see these attributes.
When I ran $xattr /Volumes/mydisk/mypdf.pdf I got this:
/Volumes/mydisk/mypdf.pdf: com.apple.Preview.UIstate.v1:
And another line about a quarantine bit
You have to do $ xattr -lv to see the full data of these extended attributes. It produces a blob of hexadecimal output for com.apple.Preview.UIstate.v1.
So I ran $ xattr -lv /Volumes/mydisk/mypdf.pdf
And copied the output. Then I opened the PDF in Preview, changed the page and closed Preview.
Then I ran $ xattr -lv /Volumes/mydisk/mypdf.pdf again
And then compared the blobs of hexadecimal output for com.apple.Preview.UIstate.v1, which were different between the two occasions.
The final test was to delete the extended attribute data:
$ xattr -c /Volumes/mydisk/mypdf.pdf
And that’s it! It’s back to page 1 when you open it in Preview
It appears the last page viewed of a PDF is stored in these extended attributes. I’m so happy!!
Best Answer
You could convert them all to ePub using Calibre. Add the ePubs to iTunes and they should sync with iBooks. As not all PDFs are formatted the same, some will show the generic cover while some will show the first page when converted to ePub. You can change the cover art for each book individually in iTunes, by selecting the book > Right click > Get Info > Artwork.