Can try this...
https://social.technet.microsoft.com/Forums/systemcenter/en-US/94d36993-2aa1-4805-b3f9-f1670ad1a0a6/the-need-to-force-a-refreshservercompliancestate-on-all-systems?forum=configmgrsum

create a VB script that does something like :

' Initialize the UpdatesStore variable.
    dim newCCMUpdatesStore

    ' Create the COM object.
    set newCCMUpdatesStore = CreateObject ("Microsoft.CCM.UpdatesStore")
    ' Refresh the server compliance state by running the 
RefreshServerComplianceState method.
    newCCMUpdatesStore.RefreshServerComplianceState

    ' Output success message.
    wscript.echo "Ran RefreshServerComplianceState."

________________________________
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CO CITRIX/SERVER
Insurance Australia Group Limited
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PLEASE CONSIDER THE ENVIRONMENT BEFORE PRINTING THIS EMAIL.
________________________________

From: [email protected] [mailto:[email protected]] On 
Behalf Of greg franklin
Sent: Wednesday, 4 February 2015 7:02 AM
To: [email protected]
Subject: [mssms] patch issue

Hey Guys,

We are in SCCM 2007 R3 environment.Recently we are facing with one issue.

The issue is One of my client server inventory on SCCM is reporting that it is 
missing 3 patches,which were already targeted previously.

When we connected the machine, it appears these patches have been installed.But 
for that particular server those 3 patches are showing as required.Patches 
which are targeted after targeting those 3 patches are working fine.

I am not sure if SCCM is just not processing it's record properly, or if the 
patch is not installed correctly or what.

what would i do now.any assistance will be highly appreciated

Thanks & Regards,
Greg
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