Its not starting over cuz your bene bacteria is not in the water its on the lr
and some on substrate. He would only have die off if his rock dried, as long as it stays wet the bacteria can live.
Do you have fish in the tank? If you dont there could be die off because of a shortage of food for your bacteria such as ammonia and nitrite unless you dose. It takes time for shrimp to break down into ammonia.
How often have you been doing pwc
's and at what percentage?
Do you have a skimmer? Sump? Macroalgea?