If you have a single tank of ion exchange resin it is an anionic exchange resin. When it starts off, that is, when it is ready to use, the resin is in the chloride ion form. When you pass your nitrate ion containing water through it, the chloride ion is exchanged for the nitrate ion. The chloride ion comes out of the unit in the water.
When you dissolve table salt in water, it dissolves into sodium ions and chloride ions. This form of chlorine in safe to drink or for aquariums. No need for dechlor.
THe cations associated with the nitrate ions you are trying to remove are possibly sodium ions, calcium ions, magnesium ions, and some others. IF your high nitrate ion level in the source water is due to fertilizer run off, it is almost a sure thing that the form is sodium ion.
So probably your nitrate filter is being fed sodium nitrate and is coming out as sodium chloride.
If you have a double set of cylinders, the second cylinder is the cation exchange unit which starts in the sodium ion form. When water with calcium ions and magnesium ions (which are the two usual causes of hard water)are in the source water, they are exchanged for sodium ions. Sodium ion is not a hard water component. SO removing calcium ions and magnesium ions, gives you soft water.
None of the above can give you any explanation for fish die off.
Ion exchange units are very reliable and safe.
However if you are regenerating with caustic or hydrochloric acid (Muratic acid), which is done in some ion exchanges process where neither sodium ions or chloride ions are wanted, the regeneration is done with excess chemicals and it would be easy to kill fish with either caustic (sodium hydroxide) or hydrochloric acid. It is unlikely any household unit uses these processes.
If you find your unit is not using sodium chloride to regenerate your household exchange unit, what is it being regenerated with.
A malfunction of the regeneration process where an excess of sodium chloride was pumped into your water and ended up in the aquarium could be an explanation. But unlikely to occur, though the unit must be programmed to limit the amount of sodium chloride used per cycle.
A TDS (total dissolved salts) meter would quickly tell you if there were excess salt in the water. Reading up to about 1000 are fine, however.
Very high sodium chloride concentrations will cause all fish to die.
Lack of oxygen can also explain a large die off. Lack of oxygen can happen. If the fish that survive are air breathers, like gouramis or corys, oxygen level is a more likely a cause.
