I frequently flush my saltwater system with freshwater, and will occasionally follow a freshwater rinse with a diluted bleach rinse and a another freshwater rinse. If I am not in open
water that is very clear, I close the seacock and rinse with freshwater so no saltwater sits in it.
I do this simply by removing the hose from the seacock and sticking it in a small bucket.
I don't have any filters etc, as I keep the seacock closed if not in clean
water. I've not had any issues.