When Connecting to the TDS Endpoint of two specific D365 environments, using the url of the environments in question in SQL Server Management Studio, a different database seems to be shown. This is also demonstrated by the fact that I am missing (custom) tables in said database. There is an environment with the same name as the database that is being shown. That environment also does not contain any customizations. Therefore it is also logical that no custom tables are listed in Management Studio.
One thing I might add is that last week we have performed schema only copies from the environment with the same name as the database name that is shown to the environments that I am trying to access using their TDS Endpoint in Sql Server Management Studio. Maybe that is the reason for this incorrect behaviour.