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Just to expand on the situation: I added multiple bookmarks (in one case 36) to three PDFs on my Touch.
At some point every page in the three PDFs started showing dog-ears. If dismissed, the dog-ear could not be brought back. HOWEVER, the list of bookmarks in the Annotations page remained unchanged.
Unmarking a dog-ear on a page that actually had a bookmark (on the Annotations page) deleted the bookmark.
I've dealt with the problem by deleting all bookmarks for those three pdfs using sqlitemon. Going forward, I'm going to backup the database after I annotate each book. It'll be interesting to see if the problem reoccurs.
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