Hello Eason, thanks for your comment! So, if I understand your comments correctly, I DO need to use the "UseDefaultSQLPaths" paramater and that will NOT use the default instance or a default path like "program files\sql...", but the path I set for the data and log files during installation? Just to make sure Iam not messing up my sql machine ;-)
The command would be:
Install-CsDatabase -Update -ConfiguredDatabases -SqlServerFqdn <EEBE.Fqdn> -UseDefaultSqlPaths
and it will upgrade/ install the databases that were stored in d:\apps\sqlserver\... to d:\apps\sqlserver\ as configured and NOT in c:\programfiles\sql...