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There are 2 parts to a possible solution:
- Since Tableau won't let you use the same file for input and output in the same flow, you'll need to create a copy of the new master file each time you run the flow. You can automate this via scrip that runs the flow, then copies the output to a different location to be used as the new Master input for the next time. you can find help for command line scripting here: Save and Share Tableau Prep Work - Tableau
- Use a pattern in your flow that brings in the existing records (from the copy) and new/updated records from the source. Then you'll match where possible, updated where needed and union together with anything new. The pattern will look something like:
Hope that helps!