I don't understand your comment fully. DE itself doesn't 'write over'
So, every time you change the bookmarks in the program or close the program, DE alters the "annotations" file to represent whatever is in the program at that time. If the program opens without accessing the annotations file, it will register that no bookmarks exist. I don't know why, but one of the times that I opened DE, it didn't access annotations, so when I closed it, because I thought if I closed it and reopened it the bookmarks might come back, it created a new annotations file that says there should be no bookmarks.
There are a couple of Adobe employees that read posts here. Perhaps they
can address this....
Guys - are you listening?
I think the best I'm going to do is the backed up version of the annotations file from a scheduled system backup. I'll copy those over to the hardcopy of the book (which I still have), and then spend a few hours recreating the others, after which I guess I'll either back up every time I annotate or, more likely, get back to book highlighting (which I was going to do eventually anyway, due to limitations on annotations in DE). The main remaining benefit of the DE is transportability, which will still be useful, just not quite as useful as I'd hoped when I initially got the product. Thank you for the support, if Adobe does have any better solutions, I'd love to hear them.