Hi Emil,
Thanks for getting in touch! I’m just messaging in here quickly to let you know I’ve responded to your other related question in the other thread, and we can continue digging into the solution there. 
One thing I forgot to address is your mention that your export of the variable set variables come out with just the LibraryVariableSet definition, instead of the expected variables. I think the same thing happened in my testing when I attempted to hit libraryvariablesets/LibraryVariableSets-ID endpoint instead of variables/variableset-LibraryVariableSets-ID endpoint.
Hope that helps!
Best regards,
Kenny