Yes, I concur about this not being an iCloud issue. I have several more apps - keepit, agenda, devonthink, that successfully sync their databases using iCloud between multiple IOS devices and 2 macs.
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I have been having a fairly seamless experience in my imac annotating/exporting from 3 pdf textbooks stored on icloud. However, when I open the app on my ipad, I have a problem with the textbooks. I see the 3 tabs with the textbook names, but there is no actual book content. All of my annotations and mindmap items appear correctly…just no textbook content. Wondering what am I missing…
Not sure if this problem is the same as yours, because clearly SOME of my content is syncing. Indeed, this is very frustrating!
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FWIW, a user’s guide of sorts is now on Google drive. I don’t see anything about syncing with iOS, though.
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iOS device: click EXPORT. Then export the notebook to DropBox. Macbook: Go to DropBox and click the exported notebook—it will automatically open to the Mac version of the app. Problem solved. This is a workaround. The apps, both iOS and MacOS should sync without any problem, but as we all know, some notebooks are not appearing on the mac version. This is the solution I discovered.