Answer:
You cannot. This is the reason why tunnel pasteurizers have been the prevalent pasteurization technology for brewing, and why the major breweries in the Americas continue to support tunnel pasteurization. The only options you would have are to install a clean room, sanitary filler, do regular QC swabs, have your product coded by batch, and (likely) install a warmer if you are filling and packaging significant quantities.
You should also consider beer waste. As the flash pasteurization loop cannot be empty with each start and stop of the system water or beer need to be recirculated. This indicates that you will either send beer to drain with each start and stop (as the unit is flooded with water to be recirculated) or you will run beer in a loop effectively pasteurizing it dozens of times and then return it into the production, which shoot holes in the flavor argument for flash pasteurization.
You can find detailed information on the comparison of tunnel and flash pasteurization at www.pasteurizers.info.