Ok, no answers..
For those how have the same question. This maybe help with some clarity about the consequences of cloning in VMware.
https://social.technet.microsoft.com/Forums/ie/en-US/2eb10003-3f92-4549-b3d9-ef629bd9f3eb/changing-s...
SID:s always duplicated. If you have duplicated SID:s in your environment , it´s looks that is asking for troubles,
You maybe think, then I change the SID of my cloned VM?
The problem is that your clone have to leave the domain and join WORKGROUP and
then run sysprep (the only official and supported solution from Microsoft)
If you have SQL databases and certain applications already installed, then be prepared
for the next level of problems. (Google on that)
Example:
https://social.technet.microsoft.com/Forums/ie/en-US/2eb10003-3f92-4549-b3d9-ef629bd9f3eb/changing-s...
Conclusion:
To reach a stable and working "clone" I have to get back to start and deploy from template a new VM, and install everything from scratch.
Only hard work is the right way to go of making a "duplicated" copy of your already preinstalled apps and database server.