You can use the REST API to clear all alerts. There are two relevant calls: queryAlert and modifyAlerts
Here is an article (in German) by Frank Bess with an example python script closeAlerts.py (look for a ZIP link at the end of the article): http://vgeht.de/2015/11/10/alarm-alarm-die-huette-brennt/ - the script can be executed on vR Ops system itself. Please read the readme.txt carefully.
Usage: ./closeAlerts.py –vrops=MYVROPSHOST –uid=admin –pwd=THISISMYPWD