I appreciate your suggestions but I confused. I am having this same issue. I have dozens of books and probably a hundreds personal PDF's iBooks that I downloaded from Mail or from the Internet. Probably for the last few months, I have not been able to "Open in" iBooks for PDF's from Mail or the internet. When I am in a PDF in Mail or internet and I click on 'Open In", iBooks opens temporarily and I see the new PDF appear in the bookshelf for a second or two and then it disappears. I have no problem however using Open In to save PDF's to any other 3rd party App such as Annotate +, Good Reader, Notability and many others. After this issue started I used to be able to get the Open In iBooks function to work if I tried it multiple times.Sometimes it would work on the 4th or 5th try, sometimes the 2nd, and sometimes I would try 10 times and finally just give up and save it to Annotate+. I tried some tricks that seemed to work sometimes. Like making sure I would close the iBooks app in the multi-task bar before using the Open In iBooks function. Sometimes that seemed to work. Now nothing works. I've tried dozens of different PDF's from Mail or Safari dozens of times each and nothing will "Open In" iBooks anymore. This really ***** as iBooks is my preferred storage and reader for PDF's. I only us Annotate + when I need to edit or annotate a PDF which is pretty rare. Typically I am just saving to read them for work or personal use. iBooks is the best PDF reader in my opinion, when it works. I dont ever sync my iPad with my Mac anymore since iCloud. I have everything backed up to iCloud. No reason to sync with my Mac and take up valuable space and effort.
I haven't synced with my Mac in at least a few months. Anyway, I am afraid to delete the iBooks apps because Im not sure what will happen to all of my PDF's in iBooks. Not worried about the books which I can just download again from iBooks store. I could sync with my Mac to backup my PDF's but I believe that you also mentioned in your post that we should delete iBooks backups on our PC to fix this issue. I just want to ensure a way to save and backup my PDF's from iBooks before I go deleted the app and anything on my Mac. I assume that they should be backed up in iCloud. Just want to make sure.
I want to make sure that your suggested fix is the right one for my issue. Not sure if you were responding to someone else with a different issue. Also am curious what is going on here and why Apple has not addressed this issue with an update or at least a fix posted somewhere on their help website. This is a big pain in the but. Another issue that drives me nuts in the limitation of app choice when using Open In. I have hundreds of apps on my ipad and dozens that work with PDF's, Word, Excel, Powerpoints, etc. More often than not when I click on Open In, the app that I want to use is not listed as a choice. It is absurb to have to delete all of the apps in the list until I get the one I want to use to appear. How can Apple have not fixed this issue in the many years that the Open In feature has been available on the iPhone and iPas is astonishing to me? Don't Apple employees have this same problem and submit a feature request? Don't they read the hudreds of posts on here regarding these issues for the last few years? If they really want the iPad and iPhone to be serious business tools, these issues need to be fixed. People can't have randomness decide what app they use to open a file from an email attachment or Safari. Just venting. Sorry.