Embedded database is only for testing, it’s not supposed to be used in production environment. It’s not easy to clean this database and not to brake anything. Monitoring plugin doesnt have logs cleaning option, so when deleting something manually in the database there is a chance to brake something. I think in your case the only solution would be to start with a fresh database (some standalone preferable, like MySQL). In future you should make backups and check if everything is working fine after you manually edit your database. Probably you shouldnt use Monitoring plugin if you need to delete logs. Though there is no other convenient solution. You can only use audit logs and audit logs viewer, but it is not very convenient and you cant search in all logs.
I’m saying that, because there is noone here who understands how this plugin works. Jive developers (who have created this plugin) have open sourced it and left it as is. I doubt you will get any solution for this problem.