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Hi Patrick and Christine,
Did you find a resolution to this? I have the exact same issue and Support have not been able to resolve it yet. I am currently getting around this by using a batch file and Windows Task Scheduler to move the files to an archive folder before the Scheduled Prep flow on Server runs each night.
No I did not get this fixed at all. The help team said it was a problem at my end and would not look into it any further.
I have the same issue. I have solved the issues with input files in network drives by using UNCs instead of drive letters, but as far as output files are concerned I have now to move them out of the output directory otherwise the flow will not run.
Tableau Prep is full of bugs and I do not have the time to open a support ticket each and every time an issue arises.