I've recently updated to the new Bookends for ios so I can give my related two cents on this. I have a related issue with highlights lost.
I began losing highlights with the latest Bookends on Tap update on ios 10. This did not happen before (not sure if it was an issue with ios10 or BoT).
In this case, BoT would simply crash and lose the highlights.
Upon updating to the new Bookends for ios, the problem went away, only to return in a different way. In this case, Bookends would not crash, but the Bookends pdf viewer would. Essentially, the viewer would disappear, being replaced by the Bookends reference detail view. On opening the pdf again, the recent highlights were lost. Regularly closing the Bookends pdf viewer and reopening after some highlighting/note-taking seems to take care of the problem and work as a kind of 'save' function.
What I managed to gather:
- I cannot find a relationship between the crashing/lost highlights and the pdf. It happends with both ocr'ed and native text pdfs. With pdfs from archive.org and scanned by me and ocr'ed in acrobat.
- The only relationship I could find is that it happens with long book-sized texts, but I believe this has more to do with the amount of highlights one ends up producing than with the pdf itself (since it will happen both with a 1mb pdf and a 200mb pdf). It seems the more highlighting one does in a file, the more prone to crashing the viewer becomes (and consequent annotation loss).
- I do not believe it has anything to do with ios or the bookends pdf framework (unless the upstream version is more recent). A simple way to make sure you don't lose highlights is to open the pdf in an external app. In my case I would open it up in 'PDF Viewer' which is an app by the same people that provide the pdf framework that Bookends uses (
https://pdfviewer.io). The same file that would cause BoT to crash and lose highlights would not have the same effect on 'PDF Viewer'.
Hope this helps a bit.
Joao