books that i purchased are not showing up on my iPad

Your response looks like it's for iBooks purchases. I believe what the question is, books purchased "online" such as from Kindle or elsewhere. I too have this problem where the books that I purchased from another source (not iBooks) but that I have imported into iBooks with the correct epub format are not syncing in iPad. Apparently they're supposed to according to all the literature that says it will along with PDFs, and I was able to have them sync before, but now it's not working. They're readable in iBooks on my MBP late '09 with El Capitan, but they're not on iPad 4 iBooks. I've double checked every possible sync settings in iBooks on MBP and in iPad, as well as sync settings in the iPad Settings>iBooks. I've restarted both device and MBP. I even looked in the cloud to see if there was an iBooks icon - nope.

Please advise if you have any insight. Thanks!

You are using the same account in the iBookstore on your iPad as you are on your Mac, and they dont show in the Purchased tab in the iBooks app on the iPad for redownloading ? You've tried logging out (e.g. tap on your id at the bottom of the Featured tab) and back into the account on the iPad to see if they then show ?

I'm trying to figure out what I may have done inadvertently to cause this, if I did. For example, I relocated my ePub files into my Digital Editions folder in my Documents so I could organize all my ebooks in their perspective folders (ePub library, Kindle content, PDFs, etc). Is it possible that iBooks sync function is confused by this? There seems to be no consensus on where iBooks stores the book files other than it is self-contained or "an island" as one site says (https://goo.gl/jJrU3S). But when you move ebooks from iTunes into iBooks upon upgrade to El Capitan it creates that folder, correct? So maybe when I moved my epub files my sync got messed up? And if so, how do I fix this?

Thanks!

Yes, my reply is about iBookstore purchases - and as the OP hasn't replied assume that is what the question was about.

How are you trying to get them into iBooks on your iOS iPad ? They will not show in the cloud in iBooks on the iPad, nor will PDFs, only iBookstore purchases potentially will - you are connecting your iPad to your Mac and using the iPad's Books tab in your Mac's iTunes to select and sync them ?

No, because iTunes doesn't sync anything back to the iPad anymore I guess. All I know is that I somehow managed to get epubs I converted from Kindle on my iPad once before since my conversion to El Cap and now I can't and I have no idea how I did it before. Magic I guess. If you have any ideas how, I would appreciate it. Otherwise I see another thread of yours says to email them to myself individually? As in, every single document I acquire that isn't from iTunes I must do this individually? Great. Way to go Apple.

The epubs are in the iBooks app on your Mac, and are readable in it ? And you've tried connecting the iPad to your Mac, selecting the iPad's Books tab in your Mac's iTunes, and selected those books and applied/synced that selection ?

Yes, they're readable in iBooks on Macbook.

Are you referring to the iPad's Settings>Summary>Books? Or the On My Device>Books?

Because if I'm in the Settings menu, in order to Sync Books, iTunes wants to remove all my books "Are you sure you want to remove existing music, movies, TV shows, books, and tones from this iPad and sync with this iTunes library?" And what is it going to sync with? Because the library in that tab shows all the same books that are On My Device. Nowhere am I seeing an option to sync it with iBooks on my OS X now that it's a separate app.

So no, I don't want to do this because I have no idea what iTunes is replacing iPad with when you consider that there is no Books library in iTunes on my Macbook anymore.

Would you please clarify? Thanks.

With the iPad connected and selected in your Mac's iTunes, I'm referring to the Books tab under the Settings heading e.g.

That tab, if the 'sync books' tickbox is ticked, will show the books that you have in the iBooks app on the Mac and let you select and sync them to the iPad's iBooks app.

If you are getting a message about removing all current content from the iPad then that isn't the computer that you sync the iPad to ?

We have success! Yes, I had been syncing the two already so I did not trust it to wipe all my content from the iPad. So in light of your last reply, I imported another "A" title into iBooks so that I could be sure iTunes was in fact looking at my iBooks app and it was there among the grayed out books. So I synced it and what do you know, it worked. 😮 Me of little faith! Thanks for sticking with the thread.

p.s. I realized I had used Dropbox to open them on iPad before. Not exactly optimal.