Hi ROEL BERGS,
I think your problem was understand the logic of this workaroud and the correct configuration.
When you created the first instance with new build it became your DEFAULT instance for this version.
The new instances of this version will have a folder in the path
C:\Program Files\Microsoft Dynamics NAV\71 - Build 36703\Service\Instances\
where the name of the folder will be the name of the new instance, for example "SecondNewInstanceName"
inside that forder you will have 3 configuration file:
1) ConfigSettings
2) SecondNewInstanceName
3) Tenants
It's important that in the SecondNewInstanceName.config the node appsettings and tenants will contain the path of the files inside this folder and in CustomSettings.config the ServerInstance will be your DEFAULT instance of the new build.