The main purpose of the freshwater flush is to keep biological growth at bay. The water in your system, and mainly your RO (Reverse Osmosis) membrane will start to grow bacteria within a couple of days if seawater is left in the system. Therefore, the factory suggests doing a freshwater flush after every use. With freshwater in your system, you will typically be growth free for 5 to 7 days. If you purchase the Z-Ion accessory, where metal ions are added to your flush water, you will typically be growth free for a full month.
If you chose not to freshwater flush but run your system every day or so you will most likely keep growth out of your system, but you will be increasing the rate of corrosion within your system. Corrosion tends to manifest first at the high-pressure fittings and stainless-steel tubes. Fittings will corrode faster, and stainless-steel tubes can get pin-hole leaks that result in small high-pressure water-jet leaks. We have seen this pop up on systems that are as young as 4-years-old. Typically, the leak does not impact production rather just causes a mess. The solution is to replace the tubes, not the most expensive or involved service but something that could be completely avoided if flushed after every use