Tableau Prep Conductor is definitely an option to consider for automation and scheduling with Tableau Server.
I have used the command-line option with limited success, hampered by a couple of issues like the one you mentioned above. Specifically, I encountered this with wildcard unions that didn't refresh to include newly added files and created this idea: https://community.tableau.com/ideas/9149
The great thing is that the Tableau Prep developers take the ideas seriously as they mature the application, and I recently got this response on that idea:
I don't know for certain that this will solve the specific issue you mentioned above (refreshing the contents of the files as opposed to the list of files), though I am hopeful!. If your issue remains, we can continue to engage with the developers and I'm confident they'll listen!
So you are saying now there is a sever version of prep? What version does the server need to be upgraded to?
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Just fyi on the topic of Tableau Prep Conductor there is a Dev Office Hours coming up next week (Dec 11) that may be of interest...
Still on Beta, but you can try it...