Hi Wobi
This appears to be a bug, the Bookmark Folder was/should be in the SI_APPOBJECTS table in the CMS database, however it now appears to be persisted in the SI_SYSTEMOBJECTS table.
I have observed this issue when changing properties on the root Bookmark Folder in the Bookmark
Administration UI. This 'touches' the Bookmark Folder InfoObject and the platform/infostore service decides to move the Folder and its contents into a different db table.
I am investigating further
Please raise an incident with SAP
Best Regards
/Paul