Hi,
For this scenario, you can only delete the Database in the Git repository manually because when you delete the Database in Denodo Platform which is configured as Version Control System you will not be able to commit that change into the Git repository.
In addition to that, the main objective of the Version Control System is to store the copy of the previous version and to compare it with the current version, which you can always use it to revert back for future use.
You can refer the section [VCS Operations for GIT](https://community.denodo.com/docs/html/browse/7.0/vdp/administration/version_control_systems_integration/vcs_integration_features/vcs_operations_for_git) of Virtual DataPort Administration Guide for more information.
Hope this helps!