I have moved this post to the Tableau Prep area of the Community forums where it is more likely to be engaged with and responded to.
This was a known issue and resolved in Tableau Prep 2018.3.2
832070 TABLEAU PREP
Publishing a flow from the Command Prompt rather than from the Tableau Prep interface produces an error, “You don't have credentials for Tableau Server to publish extract for one or more output nodes in tfl/tflx file”, though publishing from the Tableau Prep interface using the same credentials works fine.
FIXED IN 2018.3.2
I'm having a somewhat similar issue which can be found here: Tableau Prep - Schedule with command line - Error signing in server
Hope you have better luck than I!