quite simply you dont flush it
if left off overnight, then when you run it your tds will be high this is due to a build up in the dormant system, 5 mins should see TDS return to normal then connect to DI vessel.
If you have replaced all the filters and membranes then you need to run it for approx 2 hours for everything to settle into place.
just an extra note on Merlins, i only found out a week or 2 ago that if you are producing more than 20 gallons a day you should be usuing an extra prefilter before the merlin to protect the membranes.
Darran