Well thank you MS for killing my server.
I've done exactly like advised above. Stopped the services, removed .NET 4.7 (and later on 4.6.2). Reinstalled 4.6.2 with all updates (btw. there is no repair mode!). While the .NET verification tool returnes that everything is fine:
[08/23/17,11:24:58] Install state for .NET Framework 1.0: not installed.
[08/23/17,11:24:58] Install state for .NET Framework 1.1: not installed.
[08/23/17,11:24:58] Install state for .NET Framework 2.0: not installed.
[08/23/17,11:24:58] Install state for .NET Framework 3.0: not installed.
[08/23/17,11:24:58] Install state for .NET Framework 3.5: not installed.
[08/23/17,11:24:58] Install state for .NET Framework 4 Client: installed with no service packs.
[08/23/17,11:24:58] Install state for .NET Framework 4 Full: installed with no service packs.
[08/23/17,11:24:58] Install state for .NET Framework 4.5: installed with no service packs.
[08/23/17,11:24:58] Install state for .NET Framework 4.5.1: installed with no service packs.
[08/23/17,11:24:58] Install state for .NET Framework 4.5.2: installed with no service packs.
[08/23/17,11:24:58] Install state for .NET Framework 4.6: installed with no service packs.
[08/23/17,11:24:58] Install state for .NET Framework 4.6.1: installed with no service packs.
[08/23/17,11:24:58] Install state for .NET Framework 4.6.2: installed with no service packs.
[08/23/17,11:24:58] Install state for .NET Framework 4.7: not installed.
....
08/23/17,11:25:04] Section [Registry - .NET Framework 4.5 (Wow6432Node)] - stop parsing entries
[08/23/17,11:25:04] Processing custom action 'Custom Action - .NET Framework 4.0 test application'
[08/23/17,11:25:04] ExecutablePath = 'Netfx40TestApplication.exe'
[08/23/17,11:25:04] FriendlyName = '.NET Framework 4 test application'
[08/23/17,11:25:04] TimeoutSeconds = '300'
[08/23/17,11:25:04] WaitOnExit = 'true'
[08/23/17,11:25:04] Silent = 'true'
[08/23/17,11:25:04] Launching process 'Netfx40TestApplication.exe' now
[08/23/17,11:25:04] Process successfully launched. Waiting 300 seconds for it to complete.
[08/23/17,11:25:04] Process 'Netfx40TestApplication.exe' exited with return code 0
[08/23/17,11:25:04] Verification succeeded for product .NET Framework 4.6.2
and .NET 4.6.2 is installed the CU6 setup.exe still insists that there is no .NET on the system:
C:\temp\Exchange 2016 CU6>setup.exe /PrepareSchema /IAcceptExchangeServerLicense
Terms
Für Exchange Server 2016 ist .NET Framework 4.5 oder höher erforderlich. Laden S
ie die Software von "http://go.microsoft.com/fwlink/?LinkId=260991" herunter.
Thank you very much.