What's the best method of updating a Tableau desktop dashboard when subsequent files first need to run through Prep? I need help with the overall concept of how it'll work (replace? union? blend?)

I received a file of messy data. I've created a flow in Prep to clean it up and output it to a .hyper . I connected to it in Tableau Desktop and have composed a dashboard of reports. What is the best method of updating this data quarterly? 

I receive a new (messy) file quarterly - it contains the same same set of account numbers as before + any new accounts. The data that accompanies these account numbers are things like addresses and total asset value (asset value updates each quarter). I'd like to be able to show 1) Current #accounts & Current Total Assets, and 2) show a historical view of how # of accounts and Total Assets$ change over time.