configuration for flushing and increased salinity in the tank

the salinity of the seawater we transported from the sea is around 37000 mg/l.
finally yesterday we completed the whole setup,tanks and modifications in tanks and placed a 200 L tank (for permeate storage) above the 1m3 tank. The plan was that while running the system, the permeate would fill the 200 L tank and the concentrate would return back to the 1m3 tank. When the 200 L tank was full, permeate would overflow back to the 1m3 tank.

We ran the system yesterday in this configuration. As a result, the salinity in the 1 m3 tank increases during the whole "running" (since around 150 L permeate didn't return in the 1m3 tank but was stored in the 200 L tank).
So the fact now is that after 150 L permeate is stored in the 200 L tank, the salinity in the 1m3 rises to 43000 mg/l, and this is the salinity that our membranes are required to desalinate during the whole "running".

We thought that after we flush the system, we should return the 2 streams back to 1m3 tank to decrease the salinity back to around 37000 mg/l.
We are not really sure if this is the right way to run the system.

The question is: Should we continue in this configuration, even though we run the system in extremely high salinity, which doesn't correspond to the real salinity of the seawater used? (The system can handle maximum 45000 mg/l).

One alternative would be to dilute the seawater contained in the 1 m3 tank, so that when the system reaches steady state after filling up the "permeate tank", the final concentration is 37000 mg/l as the real seawater of the region.

One extra problem we face right now is the high salinity of the permeate.
We ran the system yesterday for 2 hours using the above configuration, but we found out that the permeate quality was really high (1230 mg/l). If we run it for more time, we hope that the permeate quality will decrease. But if this is not the case, then we have to consider other issues.