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I'm aware that meddling with SharePoint databases is a big-no.

Is applying SQL Server cumulative updates to the SharePoint database instance (where sharepoint_config, content and service databases reside) is as well a big-no ?

Note: Not the SharePoint CU but the SQL Server CU's

The need is actually to keep all our SQL Server instances (SharePoint and non-SharePoint) across our organisation on same build number

Thanks.

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I dont see any problem to applying the CU on SQL server, We recently Apply the SP2 for SQL Server R2 Instances and no issue found so far.

What we did, we stop the sharepoint before applying the CU on SQL Server, this is what MSFT recommend us. If you applying the CU on the Config DB Instances then i would recommend to shut down the SharePoint completely so that no connection should made to SQL Server.

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