You should be able to clear the alerts from Prism .Also you can perform the following :
To resolve all the alerts in the Nutanix cluster, run the following command on any CVM.
code:nutanix@cvm$ for alert in `ncli alert ls | grep ID | awk '{print $3}'`; do echo "Resolving alert $alert"; \ncli alert resolve ids=$alert; sleep 2; done
Refer KB https://portal.nutanix.com/#/page/kbs/details?targetId=kA0600000008cOXCAY
Does anyone know if there's a way to do this when a cluster has more than 1,000 alerts? We had some network issue the other day and our 3-node cluster has over 150,000 alerts as a result.