I calibrated my reader a couple times with the provided solution to ensure my salinity was low. My ph was also low for sometime, when I did a WC yesterday I added some seachem reef buffer to bring it up to what my reading shows, would a low ph cause any problems? It used to read around 7.2?The lower salinity is not deadly to the fish. One way to treat parasites is by keeping them in hyposalinity at 1.009sg. I don’t know about the salinity effecting bacteria but clearly it hasn’t effected all bacteria since the tank is processing ammonia into nitrate.
However for the OP since you are running hyposalinity are you sure your salinity measuring device is properly calibrated. Your salinity could be lower than you think. I agree that although your nitrates are a problem they’re not the issue with your fish.