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SCCM SCUP and Standalone WSUS running in same domain

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Currently we deploying Windows Updates via a standalone WSUS server. Because of some pressing third party application update issues(Adobe, etc.) we are looking to use SCCM SCUP intergration to deploy only third party application updates at this time.

While I am well aware that it would be a better idea to have all updates running from SCCM... The company wants to keep the standalone WSUS to deploy windows updates. I am currently working this scenario in a test environment. I have 2 seperate GPOs, one pointing to the WSUS and one pointing to the SCCM SUP. 

My question to any one that can answer is... Will there be any conflicts with this current setup if we move this into production. Or can the WSUS and SCCM SUP co-exist as long as two GPOs are in place.

Thanks in advance.


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