Bookmarks are stored in the ~/Documents/Digital Editions/Annotations folder, backing up the folder will back up the bookmarks (and annotations -they are really just the same thing)
PS post case #'s if you don't like the response you are getting. It is a lot easier to complain to our support group when we have specific instances to talk about
Should the book then automatically 're-attach' the bookmarks? That isn't happening - I copy the book and annotations file into place, open the book, and nothing is there bookmark-wise. When I close out, the .annots file has gone from 164k down to 4k.
If ADE can't find the bookmarks it will create a (nearly) empty bookmark file. To solve this, quit ADE and then overwrite the bookmark with your saved version.
That's what I would have thought. in my case, I restore the .annot file from Time Machine, open the eBook, no bookmarks are there, then when I close, the annot file drops for 25k down to 4k.
I've repaired permissions, not sure where to go from here.
Doesn't work - I restore various versions from different date, none show the bookmarks, and all do revert back to the 4k file when closing. (Apple_Training_Series_Mac_OS_X_.annot is the name of the file, btw.)
I guess my only remaining question is whether I should trust ADE and my Mac enough to start over with new bookmarks?