When performing a project schema update, the following error appears:

Error(s) occurred while loading schema: [DFCSCHEMA] Population Exception: The object shown in the hierarchy no longer exists in schema: -Table (). -DBMSObject is not found in DFCSchema during DFC conversion <DB Instance name> <DB Instance ID>
The Database Instance the error message refers to can be edited successfully and schema can be updated in other projects where that Database Instance is used.
This is a metadata inconsistency that occurs because the Database Instance mentioned in the screenshot is not selected as an available database instance for the project, under Project Configuration.
Follow the below steps in order to resolve this issue:
Contact Strategy Cloud Support for further assistance. In order to track down the cause of the inconsistency, customers encountering this issue should make note of Schema-related changes, Object Migrations, or error messages prior to experiencing the problem. Change Journaling, if it has been enabled, can help in preserving this information.