Cubase track visibility and synchronisation are screwed up

Cubase Pro 12

I spent hours on hours to create a project to be used as a template. This template includes many hidden (not visible, even deactivated) tracks contained within folders. In other words: The project window and mix console are supposed to be completely empty.

The issue is, that on each startup all midi tracks reappear (are visible) within the project window. On top of that, after I hid these tracks manually from the project window, go to mix console and make any change in channel visibility (show or hide, manually or via preset - doesn’t matter), the midi tracks reappear within the project window (and only there).
This only happens when sync between project window and mix console is enabled or at the moment when it’s being enabled.

Any thoughts on that?