Q: How can I find my lost pdfs in ibooks (ios7 and mavericks) after updating both?

Thank you for your tips, i'm able to find all my missing pdf files from my old Mavericks backup.

I posted this independently, decided to add it here:

I know others have had this problem before but what seems to be the most promising way to fix it requires a Mac, which I don't have, so I'm begging for someone to explain to me personally how I might solve this in a simple way. I'm keeping PDFs in iBooks on my iPod Touch. Yesterday I decided to restore the iPod to get rid of the "other" taking up storage on the device. I've been backing up to iCloud instead of iTunes for a while now, so that is what I restored from. I waited while iBooks loaded up my documents, which took a few hours (I have a lot). However, even when I checked up on it while was still loading, I could actually see book icons shifting around as some disappeared, and actually caught one in the act - it had a blue "wait" line at the bottom and disappeared when it reached the end. When it seemed iBooks had finished loading what it would, many of the PDFs were there but a good number of the them were missing. Now, I've noticed from before that when I've deleted a PDF and decided to download it again later, it still opens on the same page and location in the library it was at when I deleted it. That would seem to suggest the documents are stored or "remembered" somehow in iBooks even when they're not visible. I've seen this discussion (How can I find my lost pdfs in ibooks (ios7 and mavericks) after updating both?) which suggests the way to fix it is to go on a Mac and go into Library / Containers / com.apple.BKAgentservice / Data / Documents / iBooks / Books and select "open with... iBooks." However I have Windows, not a Mac. I am trying a restore once again but am not very hopeful. What can I do to get my missing PDFs back? They are very precious to me. Do I need to get on a Mac? Will this work with a restore from iCloud? Please help!!!!

Whether your PDFs will be on your computer  will depend upon whether you had copied them off your iPod. Had you done File > Devices > Transfer Purchases when they were on it ? If you had then they should be in the Books part of your computer's iTunes library - if they are not showing in your iTunes library then check to see if they are on the computer (but not in iTunes), by default your iTunes library is stored under :

• Windows XP: \Documents and Settings\username\My Documents\My Music\
• Windows Vista: \Users\username\Music\iTunes
• Windows 7 and Windows 8: \Users\username\My Music\iTunes

If they are then add them back via File > Add To Library, or by dragging-and-dropping them into iTunes.

When you restore to an iTunes backup their covers might temporarily show in iBooks if they were on the iPad when that backup was taken, but if they are not in the Books section of that iTunes library (they are not stored in the actual backup), then the restore won't be able to cover them back, and as the restore process/iBooks discovers that their covers will disappear from iBooks.

Restoring from iCloud will not put them back on your iPad, they are not stored in an iCloud backup.

But if PDFs are not stored in iCloud backup, why did most of them come back with the restore? This is a new device, and when I set it up using an iCloud backup a few months ago, all my PDFs were transferred. Some of those same PDFs are missing now. Will leaving iBooks completely untouched during a restore help? I did just recently upgrade to ios 8.4.

I'm not aware of PDFs and/or epubs in the iBooks app being stored in any backup - they are not included in an iTunes backup (that would look for them in your iTuens library), and unless something has recently changed related to iCloud backups then only iBookstore purchases (those still in the store) will be copied back.

Not sure what you mean by 'leaving iBooks completely untouched during a restore', you can only restore to a complete backup, you can't only restore some apps and not other.

Thanks, Tom. I tried your solution and it worked for me on my MacBook Air. Now my problem is that iBooks on my phone has the same problem. I never figured out how to sync their content. The main thing is I need to restore pdfs on my iPhone iBooks.

II've just done both a restore and then reconnected to iTunes. And checked off the missing PDFs and books I wanted to put back on my iPad. I then did a sync. They still didn't show up. For one ebook I went to the original web source and re downloaded it and interestingly when moved into iBooks it had my highlights.  But the other ibook PDFs and ebook remain missing. Any suggestion?  I have an Imac with 10.7.

Hello fellow sufferers - yes, I have had the same problem. All my pdf's dissappeared from iBooks on my iPad and MacBook. I am not sure what precipitated it, as in short succession I had to replace my laptop and iPhone, and had an upgrade on the iPad. The current configuaration is MacBook Pro with OS X 10.10.5, and iPad 3 with 9.1.

Unfortunately none of the excellent fixes posted here will work for me - I work through them with mounting excitement, then the vital last step is missing. I have found a fix which does work, though very laborious. As follows:

On the MacBook - open iTunes; go to 'File'; go to 'Library'; go to 'export Library'; scroll down to 'Books' - and lo and behold I found all my pdf's. Unfortunately all were dimmed so I was not able to open or transfer them directly. But if you make a note of all the names (I used a screen shot), then go to the search function on the desktop (the magnifying glass symbol top right on mine) and type in one of the titles, the pdf will come up and I was able to drag them one at a time to a new folder I had made on the desktop. I then transferred the folder to Dropbox where I am able to read them on the iPad. Laborious or what! I suppose I could transfer them back to iBooks, but somehow I don't think I'll be doing that!

So - if all else fails, this might be a way to recover those precious pdf files

Upgrading from iOS6 to iOS 9 made my wife iPad unusably slow.  So following Apple Support advice I erased and restored it (after first backing up to both iCloud and my Mac) and in the process lost all PDFs (including irreplaceable Veterinary Conference notes which she needs for work).  Thanks for explaining how to dig them out of the backup folder on my Mac.  Boy did you get me out of the dog house

All my PDF files are gone from my iPad. Lucky for me, they are still on my Mac and also on my iPhone. I just don't have the time to read instructions here, heck isn't it why we bought Apple in the first place? Because we plug it in and everything works? Because we have better things to do than to monkey with our computers? Somehow Apple lost sight of why is it people pay so much money for their computers and devices, if something like this can even happen. As for me, I purchased 1TB of space on dropbox and moved everything over.  I will also abandon Notes, Photos, Calendar, and eventually migrate to a different platform, as many of my colleagues already have.

Try downloading a new pdf directly onto your iPad, they all magically reappear

I Have accidentally deleted all the books, PDFs etc on my iBooks app. Are they recoverable, & if so how do I do it? I am not an iPad expert! Thanks.

Thank you, Tom.  Two years later, your fix still works!