Bookmarks are stored on the Accesspoint server if the user selects "Save as server bookmark". If the QV user doesn't save on the server then the BM will be stored on the users local computer. Only document bookmarks are saved in the actual QV analytic. Your bookmarks will be retained either way with a new version as long as the document name stays the same.
We have not found much luck in retaining bookmarks when we upgrade to a new version of Qlikview.
Hope this answers your question.