Website disabled for two hours

My host conducted some sort of security scan and found what looks like a couple of hundred false positives for malware.
This happened minutes after I finished an upgrade.
You would think their antvirus software would be the very latest. Not so apparently, because they classified dome files ad containing malware that had not changed for years.
If anything good came out of this, I discovered that the PHP version in cpanel, showing as 5.2.17 has been upgraded to 5.4 but this can only be accessed through some a configuration file, which I will try and edit tomorrow.