Ok found a solution and the issue.
I don't know why exactly but the update creates a new subfolder called harbour-webcat inside the harbour-webcat folder in /home/nemo/.local/share/ .
So simply copy the *.sqlite database from /home/nemo/.local/share/harbour-webcat/QML/OfflineStorage/Databases to /home/nemo/.local/share/harbour-webcat/harbour-webcat/QML/OfflineStorage/Databases
This should restore all bookmarks again. For restoring cookies and cache copy the .QtWebkit Folder over.
This also applies for all other applications that lost their settings or history or whatever they saved (e.g. also my video player or noto)