I’m having this problem with the most recent iOS versions. My iBooks, my Notability and my eBreviary apps all routinely loose their data, and have to be reloaded from the cloud/server. Some process has to be erasing the local copy of the data. Nearly every time i open these apps, my local data has to be retrieved from the cloud somewhere.
This was not occurring with these apps prior to the recent (iOS 11?) release. I’ve looked into the Settings->General->iPad Storage->(App) Offload App possibility, but this is not set for any apps, and I do not have a more general ‘offload’ recommendation/setting to change.