The bookmarks may be just deleted / overwritten from an user within the application or from the qmc. Another possibility might be that the bookmark is invalid in any way and isn't displayed anymore.
Earlier not seldom by large shared-files is that they became corrupt but the newer tshared-files should be significantly more robust. You could try to look into them and even to repair them - at least by the older shared-files it was possible with the power-tools:
Did you restart all the Server services and even better the whole machine - to not looking for issues which are just temporary?
Does it happens only for one application or several or maybe all of them?
Does the shared-file(s) exists? Are they in general accessible (there may be any locking from the OS I/O or any security tools)? Could certain booksmarks or any other server-objects be created, changed, deleted? Any messages within the Qlik and the OS logs?
Further make sure that all releases from the desktop clients and the server are on the same level.