Have you tried these standard fixes.
When you have problems with an app it's a good idea to clear it from RAM.
Close/Clear the app: With the problem app closed, double tap on the Home button to get the multitask bar. Tap and hold on any icon in the bar until they jiggle, then tap the minus sign on the problem app. This will remove it from RAM and insure a clean start the next time you launch the app.
If that does not work try a restart,
Restart: Hold down the power button until the power off slider appears. Slide it off. When the iPad finishes shutting down, hold down the power button again until the Apple logo appears.
and then a reset if that does not work.
Reset: Hold down the power and home buttons until the Apple logo appears. The iPad will reboot. This usually takes a bit longer than a restart.
In the case of books that are apps, or books purchased from the iBooks Store, you can also delete and re-download them for free. This often fixes problems.
If that does not work, contact the app developer for the book apps.
Contact Apple's iTunes support for iBooks.
Apple has no control over whether developers choose to update their apps when iOS is updated. If some apps are important to your profession you should always confirm that they will work with the new iOS version before updating. Also, pick your apps with the future in mind. For a professional, an app that can't export it's data to a standard format is a poor choice (because programs/apps/hardware always go out of date eventually).
This is a problem that has existed since computers were invented (and probably before). As long as we insist on trying to make better stuff it won't go away.