Restore full functionality to system after valve piston repair

Thanks to this forum, I was able to repair my antiquated Rainsoft softener and hopefully get a few more years out of it. Due to the broken shear pin and piston problem, it had not cycled at all for about 10 weeks. I repaired the valve, motor and control panel and it has cycled twice now with no problems. The question is do I need to drain the hot water heater and start fresh with the brine tank or just let it do so on its own? Also,If I completely empty the brine tank, do I need to add water manually or just let the system do its thing?
Your help is greatly appreciated and the posters here (especially H2O man) just saved me several hundred dollars and I could not be more grateful for your efforts to help in this forum.