Hi Craig,
for me it sounds that you delete in the past some repositories. MaxDb removes deleted table entries asynchronously. If you stopp the database while the asynchronous delete is still active it can happen that deelted data won#t be removed anymore.
To get the system 'clean' again there are no administration commands. You have to open a customer ticket on component Bc-DB-SDB. This issue now can only be fixed by the support team.
Regards, Christiane