We were able to reproduce similar behavior and will provide fix in the next plugin release.
Here are the steps we have used to reproduce the issue with plugin version 1.1.0
1. Run workflow "Add database"
2. Remove table from SQL server
3. Restart vCO server and there is error while loading plugin configuration. Inventory also get corupted.
To avoid this error :
1. You can run "Update a database" workflow after the table has been deleted and prior to restart vCO server.
OR
2. You can run "Remove a table from a database" workflow to remove table form plugin inventory. And after that delete it physically from the SQL server.
In current state of your environment you can try to temporary create a table with the same name as deleted one.
Restart vCO server.
Rung "Remove a table from database"
Delete table from SQL server.
Hope it helps...