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When you sync, the sync goes fromSony on computer to reader... if you want collections to stick then put in collections on computer with sony software... if you put together on the reader, the computer doesn't know so syncs back with nothing in collections, probably same with bookmarks, when you sync it links to current one and then replaces with previous one from computer... others may confirm this as I don't use Sony software but I believe this is how it works by default... may be able to modify behaviour in settings/prefs on computer...
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