The parasites could just be badly stunned and the synchrometer would not detect them. They were not dead because if you came back and tested a few hours later, they would be back again.
If you want to be sure that they are all dead, you must visually verify this.
To explain further, I have zapped microbes on the slide to the point that they appeared to be dead but had not exploded. After turning the zapper off, a while later, they would recover, come back to life, and swim away.
This was one reason why some people experienced die-off day after day. There was enough microbes left alive that they would quickly repopulate.