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Do the books added by ADE appear in calibre's device view (when connected)? If they do not, then calibre thinks that they are gone and will delete them from the Sony database, removing the collections as a side effect. The Sony will scan memory and add them back when you eject the reader, but bookmarks and collections will be gone.
I ask because I have a vague memory that ADE puts books in a folder different from the Sony Reader SW and from calibre. If I am remembering correctly then that is the explanation, and there is no solution other than to not use both ADE and calibre.
This discussion points out one general principle: it isn't a good idea to use two different programs to manage your reader. There is never a guarantee that they will play nice together. You should be able to avoid this problem by importing the books from ADE into calibre, then using calibre to send them to the Sony. ADE will already have set the DRM for your Adobe ID and the Sony is already registered, so you shouldn't have problems reading DRM-infested books.
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