Hi David,
Are you sure the .php files are being removed by a malicious actor?  Are there 
log entries or other traces that indicate an exposure to an exploit?  To remove 
files from a system would leave traces of 
activity, even remotely and subsequent tampering to cover it up is usually 
clumsily executed and easily identified.
It would depend also on your specific php version but you could install suhosin 
to log any out of band activity.  If you think a malicious actor is deleting 
files, check also your database links for insertion attacks or other 
indications of attempted tampering.  I suspect an in house error such as a bad 
day for someone, or a rogue cron job, perhaps, or if you are exposed to the 
ext4 corruption bug on Linux, look there. 
Without more information, I always assume a more local problem first, as 
opposed to intrusion etc.

--
rachel polanskis
IT Consulting, UNIX & Macintosh
Greater Western Sydney
<[email protected]>

> On 2 Jun 2015, at 13:57, David Lyon <[email protected]> wrote:
> 
> Hello all,
> 
> One place I do work for is having trouble with Hacker activity.
> 
> Let's face it, there are hacker's out there trying to take down systems.
> 
> The specific issue I'm seeing is .php files vanishing from the web server.
> 
> This is annoying and I'm wondering if any others are seeing anything like
> this.
> 
> I'm also wondering what specific steps can be taken to minimise hacking
> problems.
> 
> We don't have a big budget, a counter-hacking team or anything like that.
> 
> To me it looks like the ISP may have been hacked in a similar way as
> GoDaddy was hacked in the US.
> 
> Regards
> 
> David
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