Put it in Service on the by pass valve.
Then put it into a regeneration and see if it uses that water.
If it doesn't suck the water out during the first regeneration, then check for loose brine line compression fitting nut allowing it to suck air, or a blocked injector or injector screen and fix them.
If it does suck the water out, when it is done with the regeneration, mix two cap fulls of non scented regular household bleach in a gallon of water, pour it into the water in the salt tank and do a manual regeneration. When done run water at all fixtures and see if it is softened. If it is enjoy the softened water.