Perhaps related to the Active Response bug mentioned in the comments here?

https://web.archive.org/web/20150803131317/http://www.ossec.net/?p=1135

On Tue, Jun 14, 2016 at 9:09 AM, dan (ddp) <[email protected]> wrote:
> On Tue, Jun 14, 2016 at 9:01 AM, Zeal Vora <[email protected]> wrote:
>> I'm using the latest version of OSSEC ( 2.8 ) and yes active response is
>> enabled.
>>
>
> The latest version is 2.8.3.
>
>> So currently OSSEC clients are actively blocking attacks but due to some
>> reason they have also flushed all the iptables rules from memory ( like
>> iptables -F )
>>
>
> Are there any entries in the activeresponse log file that might shed a clue?
>
>> On Tuesday, June 14, 2016 at 6:24:52 PM UTC+5:30, dan (ddpbsd) wrote:
>>>
>>> On Tue, Jun 14, 2016 at 8:17 AM, Zeal Vora <[email protected]> wrote:
>>> > Hi
>>> >
>>> > We installed OSSEC in our production machines yesterday and today we saw
>>> > that all the iptables rules in all the machines were flushed. Something
>>> > similar to iptables -F
>>> >
>>> > Any idea on what can cause this ? I am aware that OSSEC active-response
>>> > can
>>> > add or remove entries from iptables but have never knew about flushing
>>> > entire iptables rules.
>>> >
>>> > Any help will be appreciated.!
>>> >
>>>
>>> Which version of OSSEC? Is active response enabled?
>>>
>>> >
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-- 
Doug Burks

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