When I first upgraded to the new version I saw that all my PDFs had to resync to my iPad (which had to be done in several goes, as they did not all copy over in one session). This was despite the fact that everything in iBooks had already been copied over to my iPad via iTunes, as I have too many books/PDFs to be selective.
What I have found is that despite those PDFs already being in Collections from the previous version of iBooks, if I - on the iPad - move them from the PDF folder to the right collection, then when I organise my bookshelf in that collection the shelf order appears to stay as I've sorted it. Obviously I have to monitor this for a while longer to see if my observation remains true, but if so, then this does solve part of the problem that I raised in my previous post.
The downside is that it is a long, tedious task to identify which PDFs in the PDF folder need to be moved where, especially as those newly moved PDFs still stay visible in the PDF folder and the collection already had those documents included from the last iBooks version. I am therefore systematically paging through all my iBook collections on my MBP, identifying which are PDFs, location them in the PDF folder on iPad and then moving them to the correct folder. My experience so far is when I arrange this newly gathered collection, then that bookshelf order has remained intact.
It is a long winded work around to solve this problem, but if it works then I will soon be able to ignore the PDF folder as before and just concentrate on my own collections. Any new PDFs added directly to iBooks on iPad will appear at the top of the screen and I can easily move them into folders. But I wish I hadn't got to go through this exercise.