I noticed there was no APi reference for acknowledge all, so I made my own code.
alerts = system.alert.queryAlertStatus(activeAndUnacked=1,clearAndUnacked=1)
for row in range(alerts.rowCount):
system.alert.acknowledgeAlert(alerts.getValueAt(row,"System"),alerts.getValueAt(row,"Path"),alerts.getValueAt(row,"State Name"))
fpmi.tag.writeToTag("[]Discrete\Ack",1)