How can I preserve PDF files in iBooks during synch or iOS updates

I have lost many important PDF files saved in iBooks collections as a result of upgrading the iOS on my iPad. How can PDF files and other free books, NOT purchased through iBooks store that are opened and stored and organized in iBooks collections be preserved/saved during iOS updates? Same question also applies to PDF files stored in other Apps like iAnnotate.

Before upgrading you should always back up your devices. If there is any problem you can then restore to the backup. pdfs do not sync across all devices. To sync pdfs you need to connect your devices to your Mac, and depending on where the pdfs are located, you either transfer them to your Mac, or sync them from your Mac to the iPad and iPhone.

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    Show PDF-file - Adobe Reader 5-0-5 - LV61.vi ‏42 KB

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