Lost PDF files

After doing a restart to resolve another issue I found all my PDF files in iBooks were deleted. This has happened before. Does anyone know why Apple hasn't resolved this issue?

What do you mean by 'restart' ? If you restored to a backup then PDFs are not included in a backup, neither iCloud nor iTunes. Have you got copies of them in the Books part of computer's iTunes library, or if using a Mac with Mavericks or Yosemite on it in its iBooks app so that you can sync them back ?
When you have PDFs and/or epubs in the iBooks app on your iPad, then even though they aren't iTunes purchases doing File > Devices > Transfer Purchases should copy them over to your computer's iTunes library (and if using a Mac with iBooks on it then do File > Move Books From iTunes in its iBooks app) so that you have a backup copy of them and can resync them back to a device.

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